What changed in this filing

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Item 1. Financial Statements

2025-05-06 compared with 2024-11-12 · 334 added, 464 removed, 376 unchanged (68% of the section changed)

2 unchanged sentences

Condensed Consolidated Balance Sheets

(in thousands, except per share data)

As of September 30, 2024 As of December 31, 2023

(in thousands, except share data)

As of March 31, As of December 31,

Current assets:

Cash and cash equivalents $ 312,420 $ 561,572

Marketable securities 204,502 —

Accounts receivable, net 26,293 21,857

6 unchanged sentences

Intangible assets, net 68,756 72,510

Goodwill — 49,238

Other non-current assets 46,778 55,336

20 unchanged sentences

Accumulated deficit ( 5,928,514 ) ( 5,837,557 )

Accumulated other comprehensive income 263 1,484

Accumulated other comprehensive loss ( 850 ) ( 1,806 )

Total stockholders’ equity 647,427 716,058

3 unchanged sentences

Condensed Consolidated Statements of Operations and Comprehensive Loss

(in thousands, except per share data)

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

(in thousands, except share data)

Three Months Ended March 31,

Cell Engineering revenue (1)

1 unchanged sentence

Biosecurity revenue 10,088 10,055

Product — 6,495 — 28,949

Service 13,957 11,759 44,013 71,196

Total revenue 48,318 37,944

Costs and operating expenses:

Cost of Biosecurity product revenue — 906 — 7,481

Cost of Biosecurity service revenue 9,987 6,017 30,996 39,913

Cost of Biosecurity revenue 7,957 9,202

Cost of other revenue 4,090 —

1 unchanged sentence

General and administrative 49,043 70,287

Impairment of lease assets — 96,210 — 96,210

Goodwill impairment — — 47,858 —

Restructuring charges 5,273 —

3 unchanged sentences

Interest income, net 6,081 11,711

Loss on equity method investments — — — ( 1,516 )

Loss on investments ( 3,693 ) ( 2,544 )

Loss on deconsolidation of subsidiary ( 7,013 ) — ( 7,013 ) —

Change in fair value of warrant liabilities — 940

Other income, net 1,572 2,893 2,821 9,045

Other income (expense), net ( 4,289 ) 2,015

Total other income (expense) ( 1,901 ) 12,122

Loss before income taxes ( 90,869 ) ( 165,880 )

Income tax expense (benefit) ( 375 ) ( 22 ) ( 154 ) 127

Income tax expense 88 31

Net loss $ ( 90,957 ) $ ( 165,911 )

Net loss per share, basic and diluted $ ( 1.08 ) $ ( 6.21 ) $ ( 8.58 ) $ ( 14.09 )

Net loss per share:

Basic $ ( 1.68 ) $ ( 3.31 )

Diluted $ ( 1.68 ) $ ( 3.32 )

Weighted average common shares outstanding:

3 unchanged sentences

Net loss $ ( 90,957 ) $ ( 165,911 )

Other comprehensive income (loss):

Other comprehensive (loss) income:

Foreign currency translation adjustment 849 ( 3,035 )

Reclassification of foreign currency translation adjustment realized upon sale of foreign subsidiary 1,492 — 1,492 —

Total other comprehensive income (loss) 1,986 ( 1,599 ) ( 1,221 ) ( 267 )

Unrealized gains on available-for-sale securities 107 —

Total other comprehensive (loss) income 956 ( 3,035 )

Comprehensive loss $ ( 90,001 ) $ ( 168,946 )

(1) Includes related party revenue of $ 46,659 and $ 8,727 for the three months ended September 30, 2024 and 2023, respectively, and $ 51,990 and $ 19,912 for the nine months ended September 30, 2024 and 2023, respectively.

(1) Includes related party revenue of $ 8,098 and $ 733 for the three months ended March 31, 2025 and 2024, respectively.

The accompanying notes are an integral part of these condensed consolidated financial statements.

1 unchanged sentence

Condensed Consolidated Statements of Stockholders’ Equity

(in thousands)

Three Months Ended September 30, 2024

Shares Amount Additional

Accumulated Deficit

Comprehensive

Income (Loss)

Stockholders’

Balance as of June 30, 2024 51,970 $ 5 $ 6,508,410 $ ( 5,673,620 ) $ ( 1,723 ) $ 833,072

Issuance of common stock upon exercise or vesting of equity awards 422 — — — — —

Settlement of contingent consideration 690 — 5,437 — — 5,437

Payment for fractional shares after reverse stock split — — ( 4 ) — — ( 4 )

Stock-based compensation expense — — 13,855 — — 13,855

Reclassification of foreign currency translation adjustment realized upon sale of foreign subsidiary — — — — 1,492 1,492

Foreign currency translation — — — — 494 494

Net loss — — — ( 56,403 ) — ( 56,403 )

Balance as of September 30, 2024 53,082 $ 5 $ 6,527,698 $ ( 5,730,023 ) $ 263 $ 797,943

Nine Months Ended September 30, 2024

Shares Amount Additional

(in thousands except share data)

Three Months Ended March 31, 2024

Amount Additional

Accumulated Deficit

Comprehensive

Income (Loss) Total

(Loss) Income

Stockholders’

1 unchanged sentence

Issuance of common stock upon exercise or vesting of equity awards 454,756 — 529 — — 529

Payment for fractional shares after reverse stock split — — ( 4 ) — — ( 4 )

Settlement of contingent consideration 24,657 — 1,877 — — 1,877

Issuance of common stock for asset acquisitions 328,321 — 15,876 — — 15,876

Issuance of common stock in exchange for services 68 — 2,500 — — 2,500

Stock-based compensation expense — — 40,782 — — 40,782

Reclassification of foreign currency translation adjustment realized upon sale of foreign subsidiary — — — — 1,492 1,492

Foreign currency translation — — — — ( 2,713 ) ( 2,713 )

Net loss — — — ( 439,495 ) — ( 439,495 )

Balance as of September 30, 2024 53,082 $ 5 $ 6,527,698 $ ( 5,730,023 ) $ 263 $ 797,943

The accompanying notes are an integral part of these condensed consolidated financial statements.

Ginkgo Bioworks Holdings, Inc.

Condensed Consolidated Statements of Stockholders’ Equity

(in thousands)

Three Months Ended September 30, 2023

Shares Amount Additional

Capital Accumulated Deficit

Comprehensive

Stockholders’

Balance as of June 30, 2023 48,869 $ 5 $ 6,280,823 $ ( 4,775,943 ) $ ( 1,300 ) $ 1,503,585

Issuance of common stock upon exercise or vesting of equity awards 440 — 55 — — 55

Settlement of contingent consideration 11 — 960 — — 960

Stock-based compensation expense — — 52,573 — — 52,573

Foreign currency translation — — — — ( 1,599 ) ( 1,599 )

Other comprehensive loss — — — — ( 3,035 ) ( 3,035 )

Net loss — — — ( 165,911 ) — ( 165,911 )

Balance as of September 30, 2023 49,320 $ 5 $ 6,334,411 $ ( 5,078,834 ) $ ( 2,899 ) $ 1,252,683

Nine Months Ended September 30, 2023

Shares Amount Additional

Capital Accumulated Deficit

Balance as of March 31, 2024 50,840,607 $ 5 $ 6,445,255 $ ( 5,456,439 ) $ ( 1,551 ) $ 987,270

Three Months Ended March 31, 2025

Amount Additional

Accumulated Deficit

Comprehensive

(Loss) Income Total

Stockholders’

1 unchanged sentence

Issuance of common stock upon exercise or vesting of equity awards 332,461 — — — — —

Tax withholdings related to net share settlement of equity awards — — ( 23 ) — — ( 23 )

Settlement of contingent consideration 11 — 3,222 — — 3,222

Issuance of common stock for asset acquisitions 70 — 3,581 — — 3,581

Issuance of common stock in exchange for services 51 — 2,500 — — 2,500

Stock-based compensation expense and other — — 188,029 — — 188,029

Foreign currency translation — — — — ( 267 ) ( 267 )

Release of 18,265 common shares from escrow related to acquisition — — 939 — — 939

Stock-based compensation expense — — 20,431 — — 20,431

Other comprehensive income — — — — 956 956

Net loss — — — ( 90,957 ) — ( 90,957 )

Balance as of September 30, 2023 49,320 $ 5 $ 6,334,411 $ ( 5,078,834 ) $ ( 2,899 ) $ 1,252,683

Balance as of March 31, 2025 54,698,246 $ 5 $ 6,576,786 $ ( 5,928,514 ) $ ( 850 ) $ 647,427

The accompanying notes are an integral part of these condensed consolidated financial statements.

2 unchanged sentences

(in thousands)

Nine Months Ended September 30,

Three Months Ended March 31,

Cash flows from operating activities:

3 unchanged sentences

Stock-based compensation 20,431 40,782

Goodwill impairment 47,858 —

Restructuring related impairment charges 4,823 —

Loss on investments and equity method investments 16,282 46,331

Loss on deconsolidation of subsidiary 7,013 —

Loss on investments 3,693 2,544

Change in fair value of notes receivable 5,285 —

Change in fair value of warrant liabilities — ( 940 )

Change in fair value of contingent consideration liability 3,698 10,217

Change in fair value of contingent consideration ( 1,302 ) ( 926 )

Non-cash lease expense 7,379 5,637

Non-cash in-process research and development — 16,816

Impairment of long-lived assets — 121,404

Other non-cash activity 149 ( 442 )

Changes in operating assets and liabilities:

Accounts receivable ( 6,101 ) 21,168

Accounts receivable ($(291) and $372 from related parties) ( 4,693 ) ( 6,770 )

Prepaid expenses and other current assets 462 1,154

3 unchanged sentences

Deferred revenue, current and non-current ($(7,878) and $(223) from related parties) ( 12,471 ) ( 2,912 )

( 67,779 ) ( 29,382 )

Operating lease liabilities, current and non-current ( 4,790 ) ( 4,097 )

2 unchanged sentences

Cash flows from investing activities:

Purchases of marketable debt securities ( 191,182 ) —

Purchases of property and equipment ( 7,622 ) ( 6,710 )

Business acquisition — ( 5,400 )

Proceeds from sales of marketable securities 3,951 —

Proceeds from sale of equipment 591 3,000

Other 538 336

Net cash used in investing activities ( 198,684 ) ( 12,110 )

3 unchanged sentences

Contingent consideration payment — ( 621 )

Other ( 4 ) ( 604 )

Net cash used in financing activities ( 207 ) ( 845 )

13 unchanged sentences

(“Ginkgo” or the “Company”) is to make biology easier to engineer.

The Company designs custom cells for customers across multiple markets.

The Company provides biological research and development services for customers across multiple markets and industries.

Since inception, the Company has devoted its efforts to improving its platform for programming cells to enable customers to leverage biology to create impactful products across a range of industries.

The Company’s platform comprises (i) equipment, robotic automation, software, data pipelines and tools, and standard operating procedures for high throughput cell engineering, fermentation, and analytics (referred to collectively as the “Foundry”), (ii) a library of proprietary biological assets and associated performance data (referred to collectively as “Codebase”), and (iii) the Company’s team of expert users, developers and operators of the Foundry and Codebase.

With a mission to make biology easier to engineer, the Company has recognized the need to invest in biosecurity as a key component of its platform.

The Company’s Biosecurity business is building a global infrastructure for biosecurity to empower governments, communities, and public health leaders to prevent, detect and respond to a wide variety of biological threats.

The Company’s biosecurity business (“Biosecurity”) consists of the Company’s biomonitoring and bioinformatics support services, offered to both government and non-government customers through the Company's two core offerings:

Canopy and Horizon, which provide services to government and commercial customers working to identify, monitor, prevent, mitigate, and ultimately protect humanity from biological threats.

Basis of Presentation

2 unchanged sentences

In the opinion of management, all normal recurring adjustments necessary for a fair presentation have been made.

These condensed consolidated financial statements should be read in conjunction with the Company's 2023 Annual Report on Form 10-K.

These condensed consolidated financial statements should be read in conjunction with the 2024 Annual Report.

Interim results are not necessarily indicative of results for a full year.

Reverse Stock Split

On August 19, 2024 (the “Effective Date”), with the approval of the Company's board of directors and shareholders, the Company effected a one-for-forty (1:40) reverse stock split (the “Reverse Stock Split”) for the Company’s common stock (inclusive of Class A common stock, Class B common stock and Class C common stock, par value $0.0001 per share).

Accordingly, all common shares, common stock equity awards and common stock per share amounts presented herein have been retrospectively adjusted to reflect the Reverse Stock Split.

On the Effective Date, every forty shares of common stock issued and outstanding immediately prior to the Effective Date were automatically combined into one share of such class of common stock without any change to the par value per share.

The number of shares reserved under the Company’s equity plans and the number of shares underlying awards outstanding under the Company’s equity plans was reduced proportionately.

No fractional shares were issued in connection with the Reverse Stock Split.

Shareholders entitled to receive a fractional share as a result of the Reverse Stock Split received a cash payment in lieu of such fractional shares.

The number of authorized shares of common stock was not reduced.

In respect of the underlying common stock split, an adjustment to the exercise price of the Company’s warrants (the “Warrants”) and the number of shares of the Company’s Class A common stock issuable on exercise of each Warrant was adjusted in proportion to the Reverse Stock Split.

As of the effectiveness of the Reverse Stock Split, the exercise price to purchase one share of Class A common stock equals $ 460.00 ($ 11.50 per Warrant).

Each Warrant equals one-fortieth (1/40) of one share of Class A common stock ( 40 Warrants must be exercised for one share of Class A common stock).

No fractional shares of Class A common stock will be issued upon exercise of the Warrants;

therefore, a minimum of 40 Warrants must be exercised to receive any entitlement.

For the avoidance of doubt, no other amendment, modification, alteration or change was made to the terms of the Warrants as a result of the Reverse Stock Split.

Principles of Consolidation

1 unchanged sentence

All intercompany accounts and transactions have been eliminated.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Reclassifications

Certain prior year amounts have been reclassified for consistency with the current year presentation.

In the accompanying condensed consolidated statements of cash flows for the nine months ended September 31, 2023, (i) $ 0.9 million was reclassified from non-cash customer consideration to other non-cash activity and (ii) $ 0.1 million was reclassified from other financing activities to proceeds from exercise of stock options.

The total cash used in operating and financing activities for the nine months ended September 31, 2023 is not changed as a result of these reclassifications.

Use of Estimates

5 unchanged sentences

Significant Accounting Policies

There have been no new or material changes to the Company’s significant accounting policies during the nine months ended September 30, 2024 as compared to the significant accounting policies described in Note 2 to the Company's 2023 consolidated financial statements included in the Company's 2023 Annual Report on Form 10-K.

Other than as noted below, there have been no new or material changes to the Company’s significant accounting policies during the three months ended March 31, 2025 as compared to the significant accounting policies described in Note 2 to the Company’s 2024 consolidated financial statements included in the 2024 Annual Report.

Marketable Securities

Beginning in the three months ended March 31, 2025, the Company began investing its excess cash in marketable debt securities.

All debt securities are classified as available-for-sale at the time of purchase.

Available-for-sale debt securities, including those with maturities extending beyond one year, are classified as current assets on the balance sheet due to their highly liquid nature and because they are considered available for use in current operations.

Debt securities that are highly liquid and have original maturities of three months or less at the time of acquisition are classified as cash equivalents on the

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

condensed consolidated balance sheet.

The Company considers securities to be highly liquid if they can be readily converted to cash with an insignificant risk of changes in value, typically due to active markets and high credit quality.

Unrealized gains and losses on available-for-sale marketable debt securities that are not related to credit losses are included in other comprehensive (loss) income in the condensed consolidated statements of operations and comprehensive loss.

Amortization of premium or accretion of discount, along with interest income earned on debt securities, is included in interest income, net.

Realized gains and losses, if any, are included in other income (expense), net, and the cost of securities sold is determined using the specific-identification method.

As of the balance sheet date, the Company evaluates its debt securities in an unrealized loss position to determine the extent of the loss, if any, that is attributable to expected credit losses.

Expected credit losses on debt securities are recorded as an allowance on the balance sheet, with an offsetting amount recognized in other income (expense), net, in the condensed consolidated statements of operations and comprehensive loss.

To date, the Company has not recorded any credit losses on its marketable debt securities.

Marketable securities also includes equity securities of publicly-traded companies that are considered to be available for use in current operations.

Equity securities of publicly-traded companies that are not considered to be available for use in current operations are presented within investments on the condensed consolidated balance sheet.

Recently Issued Accounting Pronouncements

There were no new recently issued accounting pronouncements that are of significance or potential significance to the Company from those disclosed within Note 2 to the Company's 2023 consolidated financial statements included in the 2023 Annual Report on Form 10-K.

Acquisitions and Divestiture

On April 10, 2024, the Company acquired certain platform assets, including fully sequenced and isolated strains, unique gene sequences, relevant functional data and metadata, and a development pipeline from AgBiome, Inc.

(“AgBiome”), a biotechnology company in the agriculture industry.

These assets expand the Company’s proprietary unified metagenomics database.

The fair value of the consideration transferred totaled $ 18.2 million and was paid with the issuance of 0.4 million shares of Ginkgo's Class A common stock.

The Company accounted for the transaction as an asset acquisition since substantially all of the value received was concentrated in the acquired developed technology, which is being amortized over a useful life of three years .

On October 3, 2023, and in connection with the Zymergen Bankruptcy, as defined and discussed in the Company’s 2023 Annual Report on Form 10-K, the Company entered into an asset purchase agreement with Zymergen (the “Zymergen APA”) as the stalking horse bidder under Section 363 of the U.S.

There were no new recently issued accounting pronouncements that are of significance or potential significance to the Company from those disclosed within Note 2 to the Company’s 2024 consolidated financial statements included in the 2024 Annual Report.

On October 3, 2023, and in connection with the bankruptcy filing of the Company’s former subsidiary, Zymergen (the “Zymergen Bankruptcy”), the Company entered into an asset purchase agreement with Zymergen (the “Zymergen APA”) as the stalking horse bidder under Section 363 of the U.S.

Bankruptcy Code to acquire exclusive rights to substantially all of Zymergen’s intellectual property assets and certain other assets.

On January 18, 2024 (the “Closing Date”), the Company, through certain of its affiliates, completed its acquisition of substantially all of Zymergen’s assets under the Zymergen APA, and on February 5, 2024, Zymergen’s plan of liquidation was confirmed by the Bankruptcy Court.

On January 18, 2024, the Company, through certain of its affiliates, completed its acquisition of substantially all of Zymergen’s assets under the Zymergen APA, and on February 5, 2024, Zymergen’s plan of liquidation was confirmed by the Bankruptcy Court.

All of the Company’s interests in the Zymergen entities were extinguished and terminated as of February 23, 2024.

1 unchanged sentence

The total cash purchase price was $ 6.2 million, with $ 5.4 million paid at closing and $ 0.8 million released from escrow.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

allocation of the purchase price to the assets acquired and liabilities assumed as of the acquisition date primarily includes $ 19.9 million of operating lease right-of-use assets, $ 6.0 million of property and equipment, and $ 19.9 million of operating lease liabilities.

The allocation of the purchase price to the assets acquired and liabilities assumed as of the acquisition date primarily includes $ 19.9 million of operating lease right-of-use assets, $ 6.0 million of property and equipment, and $ 19.9 million of operating lease liabilities.

No goodwill or intangible assets were recognized.

Transaction costs associated with the Zymergen APA were not material for the nine months ended September 30, 2024.

Other Acquisitions

The Company completed three other asset acquisitions during the nine months ended September 30, 2024.

The aggregate purchase price for the three acquisitions was $ 19.8 million and was paid with the issuance of 0.4 million shares of Ginkgo's Class A common stock.

Each transaction was accounted for as an asset acquisition as the acquired assets, consisting primarily of intellectual property rights, did not meet the definition of a business.

The assets acquired represent in-process research and development with no alternative future use.

Accordingly, the Company recorded $ 19.8 million as acquired in-process research and development expense in the accompanying condensed consolidated statements of operations and comprehensive loss for the nine months ended September 30, 2024.

On September 30, 2024, the Company sold the equity interests of its former subsidiary Altar SAS (“Altar”) for a nominal amount.

As a result of the sale, the Company deconsolidated all of Altar's assets and liabilities from its consolidated financial statements effective September 30, 2024, and recognized a loss on deconsolidation of $7.0 million in the condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2024.

The loss on deconsolidation includes a $1.5 million reclassification of accumulated currency translation adjustments to earnings.

The sale did not meet the criteria to be reported as a discontinued operation.

Transaction costs associated with the Zymergen APA were not material for the three months ended March 31, 2024.

In the three months ended March 31, 2024, the Company issued 328,321 shares of Class A common stock to acquire certain assets, which did not meet the definition of a business for accounting purposes.

The assets acquired consisted of intellectual property with an aggregate estimated fair value of $ 16.9 million, all of which was expensed as in-process research and development in the accompanying condensed consolidated statements of operations and comprehensive loss during the period, as the assets did not have an alternative use.

Restructuring

In the second quarter of 2024, in connection with the Company’s plans to reduce operational expenditures, management, with the approval of the Board of Directors, approved a restructuring plan.

This plan includes an expected reduction in labor expenses, primarily through a workforce reduction of at least 35 %, and the planned consolidation and sublease of certain facilities.

Initial workforce reductions commenced in June 2024 and continued into the third quarter, with further reductions expected in the fourth quarter of 2024 and into 2025.

All reductions are expected to be substantially completed in 2025, subject to compliance with applicable laws.

The Company plans to consolidate certain facilities through various actions, including combining office and laboratory operations into fewer locations, subleasing unused facilities, and has taken or plans to take other related measures, such as the sale of its subsidiary, Altar, in the third quarter of 2024 (see Note 2 ).

While the Company aims to complete the majority of its facility consolidation actions in 2025, the actual timing may vary, especially for subleasing unused or underutilized facilities, which may extend beyond 2025 or may not occur prior to termination of such lease, depending on market conditions.

In the second quarter of 2024, in connection with the Company’s plans to reduce operational expenditures, management, with the approval of the Board of Directors, approved and commenced a restructuring plan.

This plan includes a reduction in labor expenses, primarily through a workforce reduction of more than 50 %, and the consolidation and subleasing of certain facilities.

Initial workforce reductions commenced in June 2024 and continued through March 31, 2025, with further reductions expected for the remainder of 2025.

All workforce reductions are expected to be substantially completed

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

in 2025, subject to compliance with applicable laws.

The Company plans to consolidate certain facilities through various actions, including combining office and laboratory operations into fewer locations, subleasing unused or underutilized facilities, and has taken or plans to take other related measures, such as the sale of its subsidiary, Altar SAS, in the third quarter of 2024.

While the Company has substantially completed the majority of its facility consolidation actions with excess space available for sublease, the actual timing for subleasing unused or underutilized facilities may extend beyond 2025 or may not occur prior to termination of such lease, depending on market conditions.

Additionally, restructuring expenses related to potential asset impairments or contract amendments or terminations for any facilities no longer in use or underutilized could be material.

The costs for the reduction in force are expected to range from $ 18.0 million to $ 22.0 million primarily in the Cell Engineering segment and consist of one-time cash severance and related costs.

The costs for the reduction in force are expected to range from $ 24.0 million to $ 26.0 million primarily in the Cell Engineering segment and consist of cash severance and related costs.

The employee termination costs are recognized as of the communication date to employees, given (i) the Company instituted a one-time employee termination benefit related to its restructuring, and (ii) the employees will not be retained to render service beyond a minimum retention period.

2 unchanged sentences

Additional charges may be incurred as the Company progresses its restructuring plan and such charges could be material.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

The following table presents restructuring costs incurred during the periods presented, which are recorded as “Restructuring charges” in the condensed consolidated statements of operations and comprehensive loss (in thousands):

Three Months Ended September 30, 2024 Nine Months Ended September 30, 2024

Employee termination costs and other $ 2,949 $ 15,192

Impairment of right-of-use asset (1)

Total restructuring $ 2,949 $ 20,015

(1) Relates to a sublease of a facility in connection with the restructuring and reflects the excess of the right-of-use asset's carrying value over its fair value, which was determined based on estimates of future discounted cash flows and is classified as Level 3 in the fair value hierarchy.

Additionally, the Company recorded a $7.0 million loss on the sale and deconsolidation of Altar as a component of other income (expense) in the condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2024.

The following table presents the change in the accrued liability balance related to the restructuring activities, which is included in “Accounts payable” and “Accrued expenses and other current liabilities” in the accompanying condensed consolidated balance sheet as of September 30, 2024 (in thousands):

During the three months ended March 31, 2025, the Company incurred $ 5.3 million of employee termination benefits and other costs, which are recorded as “Restructuring charges” in the condensed consolidated statements of operations and comprehensive loss.

Employee Termination Costs and Other

Liability balance at December 31, 2024 $ 2,854

Expenses incurred 5,273

Cash payments ( 3,772 )

Liability balance at September 30, 2024 $ 2,633

Liability balance at March 31, 2025 $ 4,355

Fair Value Measurements

The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis (in thousands):

As of September 30, 2024

Classification Total Level 1 Level 2 Level 3

Money market funds Cash and cash equivalents $ 595,003 $ 595,003 $ — $ —

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of March 31, 2025

Total Level 1 Level 2 Level 3

Cash and cash equivalents:

Money market funds $ 135,564 $ 135,564 $ — $ —

Commercial paper 39,526 — 39,526 —

Treasury securities 115,640 115,640 — —

Corporate bonds 1,417 — 1,417 —

Marketable securities:

Commercial paper 23,462 — 23,462 —

Treasury securities 99,064 99,064 — —

Corporate bonds 69,138 — 69,138 —

Marketable equity securities (1)

12,838 12,838 — —

Synlogic, Inc.

Investments 253 — 253 —

Marketable equity securities Investments 19,947 19,947 — —

Notes receivable Prepaid expenses and other current assets 523 — — 523

Notes receivable Other non-current assets 14,608 — 11,960 2,648

Marketable equity securities 2,899 2,899 — —

Other non-current assets:

Notes receivable 8,901 — — 8,901

Total assets $ 508,660 $ 366,005 $ 133,754 $ 8,901

Contingent consideration Accrued expenses and other current liabilities $ 10,296 $ — $ — $ 10,296

Contingent consideration Other non-current liabilities 4,968 — — 4,968

Accrued expenses and other current liabilities:

Contingent consideration $ 5,438 $ — $ — $ 5,438

Other non-current liabilities:

Contingent consideration 3,182 — — 3,182

Total liabilities $ 8,620 $ — $ — $ 8,620

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of December 31, 2024

Classification Total Level 1 Level 2 Level 3

Money market funds Cash and cash equivalents $ 913,729 $ 913,729 $ — $ —

Total Level 1 Level 2 Level 3

Cash and cash equivalents:

Money market funds $ 521,457 $ 521,457 $ — $ —

Synlogic, Inc.

Investments 654 — 654 —

Marketable equity securities 17,559 17,559 — —

Investments 19,190 18,401 789 —

Notes receivable Prepaid expenses and other current assets 12,293 — — 12,293

Notes receivable Other non-current assets 13,601 — 11,765 1,836

Other non-current assets:

Notes receivable 14,170 — 12,327 1,843

Total assets $ 553,424 $ 539,016 $ 12,565 $ 1,843

Public Warrants Warrant liabilities $ 3,794 $ 3,794 $ — $ —

Private Placement Warrants (3)

Warrant liabilities 1,906 — 60 1,846

Contingent consideration Accrued expenses and other current liabilities 18,468 — — 18,468

Contingent consideration Other non-current liabilities 5,805 — — 5,805

Accrued expenses and other current liabilities:

Contingent consideration $ 5,438 $ — $ — $ 5,438

Other non-current liabilities:

Contingent consideration 4,484 — — 4,484

Total liabilities $ 9,922 $ — $ — $ 9,922

(1) The fair value of Synlogic, Inc.

warrants is calculated as the quoted price of the underlying common stock, less the unpaid exercise price of the warrants.

(2) Marketable equity securities classified as Level 2 reflect a discount for lack of marketability due to regulatory sales restrictions.

(3) The fair value of Private Placement Warrants classified as Level 2 is equivalent to that of Public Warrants as the transfer of Private Placement Warrants to anyone other than the initial purchasers or any of their permitted transferees results in the Private Placement Warrants having substantially the same terms as the Public Warrants.

Transfers to and from Levels 1, 2 and 3 are recognized at the end of the reporting period in which a change in valuation technique or methodology occurs.

During the nine months ended September 30, 2024, transfers from Level 2 to Level 1 occurred due to lapse of regulatory sales restrictions on marketable equity securities.

Additionally, during the nine months ended September 30, 2024, a portion of the Private Placement Warrants' estimated fair value was transferred from Level 3 to Level 2 as a result of the Private Placement Warrants having substantially the same terms as the Public Warrants when transferred to anyone other than the initial purchasers or their permitted transferees, leading the Company to determine their fair value to be equivalent to that of the Public Warrants.

There were no other transfers between Levels 1, 2, or 3 during the nine months ended September 30, 2024 or 2023.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

The table below provides a reconciliation of the beginning and ending balances for assets and liabilities measured at fair value using Level 3 significant unobservable inputs for the nine months ended September 30 (in thousands):

(1) These securities were previously reported within investments on the condensed consolidated balance sheet and, as of March 31, 2025, are classified as current assets, as they are considered to be available for use in current operations.

(2) The fair value of Synlogic, Inc.

warrants is calculated as the quoted price of the underlying common stock, less the unpaid exercise price of the warrants.

Transfers between Levels 1, 2 and 3 are recognized at the end of the reporting period in which a change in valuation technique or methodology occurs.

During the three months ended March 31, 2025, transfers into Level 3 consisted of a note receivable that was transferred from Level 2 to Level 3 upon a change in valuation technique.

During the three months ended March 31, 2024, transfers from Level 2 to Level 1 occurred due to the lapse of regulatory sales restrictions on marketable equity securities.

There were no other transfers between Levels 1, 2, or 3 during the three months ended March 31, 2025 or 2024.

Notes Receivable Private Placement Warrants Contingent Consideration

3 unchanged sentences

Settlements and payments ( 50 ) — —

Transfers to Level 2 — ( 149 ) —

Conversion to common stock ( 10,476 ) — —

Balance at September 30, 2024 $ 3,171 $ — $ 15,264

Transfers into Level 3 6,983 — —

Balance at March 31, 2025 $ 8,901 $ — $ 8,620

Balance at January 1, 2024 $ 14,129 $ 1,846 $ 24,273

2 unchanged sentences

Settlements and payments — — ( 2,753 )

Balance at September 30, 2023 $ 9,960 $ 4,196 $ 31,326

Balance at March 31, 2024 $ 15,140 $ 1,537 $ 20,594

Notes Receivable

For all of its notes receivable, the Company has elected the fair value option, for which changes in fair value are recorded in other income, net in the condensed consolidated statements of operations and comprehensive loss.

The Company's notes receivable consisted of a senior secured note in the principal amount of $ 11.8 million and a convertible promissory note in the principal amount of $ 10.0 million, both issued by Bolt Threads, Inc.

(“Bolt Threads”).

The senior secured note bears interest at 12 % per annum, is due December 31, 2027 and is included in other non-current assets at its estimated fair value.

The convertible promissory note bore interest at 8 % per annum, was convertible into equity securities of Bolt Threads upon a qualified financing, a non-qualified financing, or special purpose acquisition company transaction, at a conversion price based on certain conditions as defined in the note agreement, or was otherwise payable on demand any time after the maturity date of October 4, 2024.

During the three months ended September 30, 2024, $10.5 million in principal and accrued interest on the convertible promissory note was converted into 2.7 million shares of Bolt Threads' common stock, which is classified as a marketable equity security.

The Company used the yield method to value the senior secured note.

For all of its notes receivable, the Company has elected the fair value option, under which changes in fair value are recorded in other income (expense), net, in the condensed consolidated statements of operations and comprehensive loss.

The Company holds a senior secured note in the original principal amount of $ 11.8 million issued by Bolt Threads, Inc., which bears interest at 12 % per annum, is due December 31, 2027, and is included in other non-current assets at its estimated fair value.

As of March 31, 2025, the Company used a discounted cash flow model to estimate the fair value of the senior secured note, incorporating significant unobservable inputs such as the recovery rate and a risk-adjusted discount rate.

These inputs reflect the Company’s own assumptions and, therefore, represent a Level 3 measurement within the fair value hierarchy.

As of December 31, 2024, the Company used the yield method to value the senior secured note.

Under this method, the estimated future cash flows, consisting of principal and interest payments, are discounted to present value using an applicable market yield or discount rate.

The market yield is determined using a corporate bond yield curve corresponding to the issuer’s credit rating category and is considered an observable market input, representing a Level 2 measurement within the fair value hierarchy.

Increases or decreases in the market yield or discount rate would result in a decrease or increase, respectively, in the fair value measurement.

The market yield is determined using a corporate bond yield curve corresponding to the credit rating category of the issuer.

The fair value of the senior secured note is based on observable market inputs, which represents a Level 2 measurement within the fair value hierarchy.

In addition to the convertible promissory note issued by Bolt Threads, the Company holds a series of convertible debt instruments issued by customers as payment for Cell Engineering services.

The Company used a scenario-based method to value the convertible debt instruments issued by customers.

Under this method, future cash flows are evaluated under various payoff scenarios, probability-weighted, and discounted to present value.

The significant unobservable (Level 3) inputs used in the fair value measurement as of September 30, 2024, included scenario probabilities ranging from 20 % to 27 %, a discount rate of 16 %, and estimated time to event date of up to two years .

The significant unobservable (Level 3) inputs used in the fair value measurement as of December 31, 2023, included scenario probabilities ranging from 5 % to 85 %, a discount rate of 17 % and estimated time to event date of one to two years .

Significant changes in these inputs could have resulted in a significantly lower or higher fair value measurement.

As of September 30, 2024, the convertible debt instruments had an unpaid principal balance of $ 13.1 million and a fair value of $ 3.2 million.

As of December 31, 2023, the convertible debt instruments had an unpaid principal balance of $ 21.0 million and a fair value of $ 14.1 million.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

The Company also holds a series of convertible debt instruments issued by customers as payment for Cell Engineering services.

The Company used a scenario-based method to value the convertible debt instruments.

Under this method, future cash flows are evaluated under various payoff scenarios, probability-weighted, and discounted to present value.

The significant unobservable (Level 3) inputs used in the fair value measurement as of March 31, 2025 and December 31, 2024 included scenario probabilities ranging from 5 % to 45 %, a discount rate of 15.5 % and estimated time to event date of approximately one year .

Significant changes in these inputs could have resulted in a significantly lower or higher fair value measurement.

As of March 31, 2025, the Company’s notes receivable had an unpaid principal balance of $ 24.9 million and a fair value of $ 8.9 million, compared to an unpaid principal balance of $ 25.1 million and a fair value of $ 14.2 million as of December 31, 2024.

Contingent Consideration

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The Company can settle a majority of its contingent consideration liabilities in cash or shares of Class A common stock at the Company’s election with the remainder payable in cash.

During the nine months ended September 30, 2024, the Company settled $ 12.7 million in contingent consideration liabilities through payment of $ 2.8 million in cash and vesting of 0.8 million shares of restricted stock valued at $ 9.9 million.

During the nine months ended September 30, 2023, the Company settled $ 4.8 million in contingent consideration liability through payment of $ 1.5 million in cash and vesting of 1.6 million shares of restricted stock valued at $ 3.2 million.

Of that amount, $ 1.4 million was recorded as an increase to the acquired intangible asset with an offset to additional paid-in-capital as the contingent consideration liability was deemed not probable of occurring.

During the three months ended March 31, 2024, the Company settled $ 2.8 million in contingent consideration liabilities through payment of $ 0.9 million in cash and vesting of 31,127 shares of restricted stock valued at $ 1.9 million.

No contingent consideration was settled during the three months ended March 31, 2025.

The fair value of contingent consideration related to earnout payments from acquisitions was estimated using unobservable (Level 3) inputs as illustrated in the table below.

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The following table provides quantitative information regarding Level 3 inputs used in the fair value measurements of contingent consideration liabilities as of the periods presented:

September 30, 2024 December 31, 2023

March 31, 2025 December 31, 2024

Contingent Consideration Liability Valuation Technique Unobservable Input Range Range

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Nonrecurring Fair Value Measurements

The Company measures the fair value of certain assets, including investments in privately held companies without readily determinable fair values, on a nonrecurring basis when events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable, or when observable price changes occur for identical or similar securities from the same issuer.

The Company measures the fair value of certain assets, including investments in privately held companies without readily determinable fair values, on a nonrecurring basis when events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable and when observable price changes occur for identical or similar security of the same issuer.

The fair value of non-marketable equity securities is classified within Level 3 in the fair value hierarchy when the Company estimates fair value using unobservable inputs to measure the amount of the impairment loss.

The fair value of non-marketable equity securities is classified within Level 2 in the fair value hierarchy when the Company estimates fair value using the observable transaction price paid by third party investors for the identical or similar security of the same issuer.

During the nine months ended September 30, 2024, the Company recorded a $ 4.9 million impairment loss related to its investment in Genomatica preferred stock.

The fair value measurement was determined using the guideline public company method under the market approach.

The significant unobservable inputs used in the valuation included the selection and analysis of guideline public companies, revenue multiple and other unobservable assumptions.

The fair value measurement is classified as Level 3 in the fair value hierarchy.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

During the nine months ended September 30, 2023, the Company received a total purchase amount of $ 11.0 million in Simple Agreement for Future Equity (“SAFEs”) from customers as prepayment for Cell Engineering services.

The Company used a scenario-based method to value the SAFEs as of each contract inception date, which resulted in total fair value of $ 4.5 million.

Under the scenario-based method, future cash flows were evaluated under qualified financing and dissolution scenarios with partial recovery and no recovery in dissolution.

The cash flows under each scenario were probability-weighted and discounted to present value.

The significant unobservable (Level 3) inputs used in the fair value measurement were scenario probabilities of 20 % to 60 %, a discount rate of 14 % and estimated time to event date of one to two years .

The Company recorded impairment losses of $5.2 million and $1.8 million related to SAFEs during the nine months ended September 30, 2024 and 2023, respectively.

The fair value was generally estimated using the scenario-based method, where various payout scenarios were probability-weighted and discounted to present value.

During the three months ended March 31, 2025, the Company recorded an impairment loss of $ 1.8 million related to an investment in the preferred stock of a privately held company after concluding that the investment had substantially no value.

During the three months ended March 31, 2024, the Company recorded impairment losses of $ 5.2 million related to Simple Agreements for Future Equity (“SAFEs”).

Fair value was generally estimated using the scenario-based method, in which various payout scenarios were probability-weighted and discounted to present value.

No impairment losses related to SAFEs were recorded during the three months ended March 31, 2025.

Marketable Securities

Investments in marketable securities, including those classified in cash and cash equivalents, are summarized as follows (in thousands):

As of March 31, 2025

Amortized Cost Unrealized Gains Unrealized Losses Fair Value

Treasury securities $ 214,662 $ 46 $ ( 4 ) $ 214,704

Corporate bonds 70,501 59 ( 5 ) 70,555

Commercial paper 62,977 17 ( 6 ) 62,988

Marketable equity securities 12,838

Total cash equivalents and marketable securities 348,140 122 (15) 361,085

cash equivalents (156,591) — 8 (156,583)

Marketable securities $ 191,549 $ 122 $ (7) $ 204,502

The amortized cost and estimated fair value of marketable debt securities, including $156.6 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands):

As of March 31, 2025

Amortized cost Fair value

Due within one year $ 315,836 $ 315,900

Due after one year through five years 32,304 32,347

Investments and Equity Method Investments

The Company has partnered with other investors to form business ventures, including Motif FoodWorks, Inc.

(“Motif”), Allonnia, LLC (“Allonnia”), Arcaea, LLC (“Arcaea”), Verb Biotics, LLC (“Verb”), BiomEdit, LLC (“BiomEdit”) and Ayana Bio, LLC (“Ayana”) (collectively “Platform Ventures”).

(“Motif”), Allonnia, LLC (“Allonnia”), Arcaea, LLC (“Arcaea”), Verb Biotics, LLC (“Verb Biotics”), BiomEdit, Inc.

(“BiomEdit”), and Ayana Bio, LLC (“Ayana Bio”) (collectively “Platform Ventures”).

The Company also partners with existing entities, including Genomatica, Inc.

(“Genomatica”) and Synlogic, Inc.

(“Synlogic”) (collectively, “Legacy Structured Partnerships”) with complementary assets for high potential synthetic biology applications.

(“Synlogic”) (collectively, “Legacy Structured Partnerships”) with complementary assets for synthetic biology applications.

The Company holds equity interests in these Platform Ventures and Legacy Structured Partnerships.

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The Company’s non-marketable equity securities consist of preferred stock of Genomatica and preferred and common stock of other privately held companies without readily determinable fair values.

Non-marketable equity securities are initially recorded using the measurement alternative at cost and subsequently adjusted for any impairment and observable price changes in orderly transactions for the identical or a similar security of the same issuer.

Non-marketable equity securities are initially recorded using the measurement alternative at cost and subsequently adjusted for any impairment and observable price changes in orderly

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

transactions for the identical or a similar security of the same issuer.

Impairment losses and adjustments from observable price changes are recorded in loss on investments in the condensed consolidated statements of operations and comprehensive loss.

The Company also holds investments in early-stage synthetic biology product companies via SAFEs.

The Company enters into SAFE agreements in conjunction with a revenue contract with a customer under which the Company grants the customer a prepaid Cell Engineering services credit equal to the principal amount of the SAFE (the “Purchase Amount”), which may be used and drawn down as payment for the Company’s research and development services.

The Company entered into SAFEs in conjunction with a revenue contract with a customer under which the Company grants the customer a prepaid cell engineering services credit equal to the principal amount of the SAFE (the “Purchase Amount”), which may be used and drawn down as payment for the Company’s research and development services.

The SAFEs will automatically convert into shares of preferred stock equal to the Purchase Amount divided by the discount price, which is calculated as the price per share sold in a qualified equity financing multiplied by a discount rate.

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The Company initially records SAFEs at fair value (see Note 4 ) and adjusts the carrying amount of the instrument at each reporting period for any impairments.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Investments consisted of the following (in thousands):

As of September 30, 2024 As of December 31, 2023

As of March 31, 2025 As of December 31, 2024

SAFEs $ 16,689 $ 16,689

1 unchanged sentence

Marketable equity securities 2,899 17,559

Genomatica preferred stock 6,985 11,885

Synlogic common stock 630 1,627

Synlogic warrants 211 238

Total $ 32,173 $ 48,704

Loss on investments and equity method investments consisted of the following (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

(Loss) gain on investments:

Synlogic common stock $ ( 4 ) $ ( 1,538 ) $ ( 998 ) $ ( 3,631 )

Synlogic warrants ( 2 ) ( 618 ) ( 401 ) ( 1,459 )

Genomatica preferred stock — ( 33,000 ) ( 4,900 ) ( 33,000 )

Marketable equity securities ( 6,906 ) 460 ( 4,771 ) ( 3,286 )

Non-marketable equity securities — ( 1,628 ) — ( 1,628 )

SAFEs — — ( 5,212 ) ( 1,811 )

Total $ ( 6,912 ) $ ( 36,324 ) $ ( 16,282 ) $ ( 44,815 )

Loss on equity method investments:

BiomEdit $ — $ — $ — $ ( 1,462 )

Other — — — ( 54 )

Total $ — $ — $ — $ ( 1,516 )

The components of loss on investments for each period were as follows (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

Three Months Ended March 31,

Impairment charges $ ( 1,844 ) $ ( 5,212 )

Realized and unrealized losses recognized on marketable equity securities ( 6,912 ) ( 1,696 ) ( 6,170 ) ( 8,376 )

Downward adjustments from observable price changes — ( 1,628 ) — ( 1,628 )

Total loss on investments $ ( 6,912 ) $ ( 36,324 ) $ ( 16,282 ) $ ( 44,815 )

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Total realized and unrealized gains and losses associated with equity investments accounted for at fair value or the fair value measurement alternative consisted of the following (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

Net realized loss recognized on equity investments sold (1)

$ ( 844 ) $ — $ ( 844 ) $ —

Net unrealized losses recognized on equity investments held as of the end of the period ( 6,068 ) ( 36,324 ) ( 15,438 ) ( 44,815 )

Unrealized gains (losses) recognized on marketable equity securities and warrants ( 1,849 ) 2,668

Total loss on investments $ ( 3,693 ) $ ( 2,544 )

(1) Reflects the difference between the sale proceeds and the carrying value of the equity investments at the beginning of the period or the acquisition date, if later.

The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of September 30, 2024, including cumulative unrealized losses, were as follows (in thousands):

As of September 30, 2024

The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of March 31, 2025, including cumulative unrealized losses, were as follows (in thousands):

As of March 31, 2025

Total initial cost $ 107,996

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Variable Interest Entities

With respect to the Company’s investments in Motif, Allonnia, Genomatica, Arcaea, BiomEdit, Verb and Ayana (collectively, the “Unconsolidated VIEs”), the Company has concluded these entities represent variable interest entities (“VIEs”).

With respect to the Company’s investments in Motif, Allonnia, Genomatica, Arcaea, BiomEdit, Verb Biotics, and Ayana Bio, the Company has concluded these entities represent variable interest entities (such entities, the “VIEs”).

While the Company has board representation on certain of these entities and is involved in the ongoing development activities of these entities via its participation on such entities’ joint steering committees (“JSC”), the Company has concluded that it is not the primary beneficiary of these entities because:

(i) the Company does not control the board of directors of any of the Unconsolidated VIEs, and no voting or consent agreements exist between the Company and other members of each respective board of directors or other investors, (ii) the holders of preferred security interests in the Unconsolidated VIEs hold certain rights that require their consent prior to taking certain actions, which include certain significant operating and financing decisions, and (iii) the Company’s representation on the JSC of each respective entity does not give it control over the development activities of any of the Unconsolidated VIEs, as all JSC decisions are made by consensus and there are no agreements in place that would require any of the entities to vote in alignment with the Company.

As the Company’s involvement in the Unconsolidated VIEs does not give it the power to control the decisions with respect to their development or other activities, which are their most significant activities, the Company has concluded that it is not the primary beneficiary of the Unconsolidated VIEs.

Additionally, the Company holds equity interests in certain privately-held companies that are not consolidated as the Company is not the primary beneficiary.

As of September 30, 2024 and December 31, 2023, the maximum risk of loss related to the Company’s VIEs was limited to the carrying value of its investments in such entities.

Refer to Note 5 for additional details on the Company’s investments and equity method investments.

(i) the Company does not control the board of directors of any of the VIEs, and no voting or consent agreements exist between the Company and other members of each respective board of directors or other investors, (ii) the holders of preferred security interests in the VIEs hold certain rights that require their consent prior to taking certain actions, which include certain significant operating and financing decisions, and (iii) the

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Company’s representation on the JSC of each respective entity does not give it control over the development activities of any of the VIEs, as all JSC decisions are made by consensus and there are no agreements in place that would require any of the entities to vote in alignment with the Company.

As the Company’s involvement in the VIEs does not give it the power to control the decisions with respect to their development or other activities, which are their most significant activities, the Company has concluded that it is not the primary beneficiary of the VIEs.

Additionally, the Company holds equity interests in certain privately-held companies that are not consolidated as the Company is not the primary beneficiary.

As of March 31, 2025 and December 31, 2024, the maximum risk of loss related to the VIEs was limited to the carrying value of its investments in such entities.

Refer to Note 6 for additional details on the Company’s investments and equity method investments.

Supplemental Financial Information

Cash, Cash Equivalents and Restricted Cash

The reconciliation of cash, cash equivalents and restricted cash reported within the condensed consolidated balance sheet to the totals shown within the condensed consolidated statement of cash flows is as follows (in thousands):

As of September 30, 2024 As of September 30, 2023

As of March 31,

Cash and cash equivalents $ 312,420 $ 840,440

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(1) Includes cash balances collateralizing letters of credit associated with the Company’s facility leases and customer prepayments requiring segregation and restrictions in its use in accordance with the customer agreement.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Supplemental cash flow information

The following table presents non-cash investing and financing activities (in thousands):

Nine Months Ended September 30,

Three Months Ended March 31,

Supplemental disclosure of non-cash investing and financing activities:

Right-of-use assets obtained in exchange for new operating lease liabilities $ 223,853 $ 13,770

Common stock issued for asset acquisitions 18,245 3,581

Purchases of property and equipment included in accounts payable and accrued expenses $ 96 $ 7,886

Return of investment in equity securities for reduction in deferred revenue 6,760 —

Common stock issued as settlement of contingent consideration liability — 1,877

Common stock issued for retention payments related to business and asset acquisitions 2,959 —

Equity securities received for Cell Engineering services 55 13,843

Convertible financial instruments received for Cell Engineering services — 5,595

Conversion of notes receivable for common stock 10,476 —

Property, Plant and Equipment, net

Property, plant and equipment, net consisted of the following (in thousands):

September 30, 2024 December 31, 2023

As of March 31, As of December 31,

Lab equipment $ 148,815 $ 150,887

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Total property, plant and equipment 361,249 364,592

Accumulated depreciation and amortization ( 150,735 ) ( 120,718 )

Accumulated depreciation ( 163,421 ) ( 160,872 )

Property, plant and equipment, net $ 197,828 $ 203,720

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Operating Lease

In April 2024, the Company commenced its 15-year lease of a new office and laboratory space located in Boston, Massachusetts.

The leased property consists of approximately 260,000 rentable square feet and is expected to be occupied by mid-2025.

The lease agreement includes an option to extend the lease for ten years at then-market rates.

The Company is not reasonably certain to exercise this option at lease commencement.

The lease is classified as an operating lease, includes a period of free rent and also tenant improvement incentives.

The lease does not contain material restrictive covenants or residual value guarantees.

Upon the lease commencement, the Company recorded a right-of-use asset of $ 213.3 million, net of lease incentives received, and a lease liability of $ 223.9 million.

The discount rate used in determining the lease liability was the Company’s estimated incremental borrowing rate of 7.8 %.

Base rent during the first lease year is approximately $ 21.1 million and is subject to annual increases of 3 % thereafter.

Exit of a Leased Facility

In September 2023, the Company’s former subsidiary, Zymergen, ceased the use of and exited a leased facility consisting of approximately 300,000 square feet of office and laboratory space in Emeryville, California.

The facility was used pursuant to an operating lease with a minimum term expiring in August 2033.

Zymergen's exit resulted in an impairment loss of $ 96.2 million, including $ 36.6 million for the right-of-use asset and $ 59.6 million for the related leasehold improvements.

The impairment loss represents the amount by which the carrying value of the assets exceed their estimated fair values as of September 30, 2023, as determined using a discounted cash flow model under the income approach.

The fair value measurements are based on significant inputs not observable in the market and therefore represent Level 3 fair value measurements.

The key inputs used in the valuation were estimated sublease rental income and a discount rate of 8.5 %.

The impairments are presented as impairment of lease assets in the condensed consolidated statement of operations and comprehensive loss for the three and nine months ended September 30, 2023.

Capitalization

The following table presents the Company’s authorized, issued, and outstanding common stock as of the dates indicated (in thousands):

The following table presents the Company’s authorized, issued, and outstanding common stock as of the dates indicated:

Authorized Issued Outstanding

Common stock as of September 30, 2024:

Common stock as of March 31, 2025:

Class A 10,500,000,000 45,955,211 43,075,350

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15,800,000,000 57,815,105 54,365,785

On April 3, 2023, the Company issued 0.1 million shares of its Class A common stock as purchase consideration for the acquisition of certain intellectual property assets of StrideBio, Inc.

Refer to Note 2 , Acquisitions, for shares of common stock issued related to fiscal 2024 acquisitions.

On May 9, 2023, the Company issued 0.1 million shares of Class A common stock, valued at $ 2.5 million, as settlement for an employee retention milestone related to the FGen AG business acquisition.

An additional 0.1 million shares, valued at $ 2.5 million, were issued on April 26, 2024 for the final milestone payable in connection with that acquisition.

Refer to Note 10 , Stock-Based Compensation, for a summary of shares of common stock issued in connection with the Company’s equity incentive plans.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Goodwill and Intangible Assets, net

All goodwill is allocated to the Cell Engineering reporting unit and segment identified in Note 12 .

Due to a sustained decrease in the market price of the Company's Class A common stock and market capitalization, the Company identified that an indicator of impairment was present as of June 30, 2024.

As such, the Company completed a quantitative impairment test related to its Cell Engineering reporting unit.

To conduct the impairment test of goodwill, the estimated fair value of the reporting unit was compared to its carrying value.

The estimated fair value of the reporting unit was determined using a weighted approach that considered a discounted cash flow (“DCF”) model under the income approach and the guideline public company (“GPC”) method under the market approach.

Significant inputs used in the DCF model included the projected future operating results of the reporting unit and the applicable discount rate, while inputs used in the GPC method consisted of a revenue multiple.

The fair value measurement of the reporting unit is classified as Level 3 in the fair value hierarchy because it involves significant unobservable inputs.

The Company reconciled the resulting fair value of its reporting unit to the market capitalization of the Company to corroborate the fair value estimate used in the impairment test.

The result of the interim impairment test indicated that the estimated fair value of the reporting unit was less than its carrying value.

As a result, the Company recorded a $ 47.9 million goodwill impairment charge during the nine months ended September 30, 2024.

Changes in the carrying amount of goodwill consisted of the following (in thousands):

Balance as of December 31, 2023 $ 49,238

Goodwill impairment (accumulated impairment loss) ( 47,858 )

Impact of foreign currency translation ( 1,380 )

Balance as of September 30, 2024 $ —

Intangible Assets, net

Intangible assets, net consisted of the following (in thousands):

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Amortization Period

September 30, 2024:

March 31, 2025:

Developed technology $ 112,648 $ ( 43,892 ) $ 68,756 6.6

$ 114,272 $ ( 34,706 ) $ 79,566 6.8

Customer relationships 380 ( 380 ) — 0.0

Assembled workforce 190 ( 190 ) — 0.0

Total intangible assets $ 114,842 $ ( 35,276 ) $ 79,566

December 31, 2024:

Developed technology $ 111,393 $ ( 38,883 ) $ 72,510 6.6

Customer relationships 380 ( 261 ) 119 0.9

Assembled workforce 190 ( 184 ) 6 0.3

Total intangible assets $ 105,849 $ ( 23,108 ) $ 82,741

(1) The gross carrying value and accumulated amortization balances include the impact of cumulative foreign currency translation adjustments.

(2) During the third quarter of 2024, the Company deconsolidated $ 8.3 million of developed technology intangible assets related to the deconsolidation of Altar (see Note 2 ).

In the second quarter of 2024, in connection with the acquisition of AgBiome, the Company acquired developed technology with an aggregate fair value of $ 18.2 million and an estimated useful life of three years .

For further information, see Note 2 .

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Amortization expense was $ 4.9 million and $ 4.0 million for the three months ended September 30, 2024 and 2023, respectively, and $ 13.3 million and $ 12.2 million for the nine months ended September 30, 2024 and 2023, respectively.

As of September 30, 2024, estimated future amortization expense for identifiable intangible assets is as follows (in thousands):

(1) Gross carrying value and accumulated amortization include the impact of cumulative foreign currency translation adjustments.

Amortization expense was $ 4.7 million and $ 3.4 million for the three months ended March 31, 2025 and 2024, respectively.

As of March 31, 2025, estimated future amortization expense for identifiable intangible assets is as follows (in thousands):

Remainder of 2025 $ 14,235

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Stock-Based Compensation

The following table summarizes stock-based compensation expense by financial statement line item in the Company’s condensed consolidated statement of operations and comprehensive loss for the periods presented (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

The following table summarizes stock-based compensation expense by financial statement line item in the Company’s condensed consolidated statements of operations and comprehensive loss for the periods presented (in thousands):

Three Months Ended March 31,

Research and development $ 8,993 $ 23,192

General and administrative 9,734 17,590

Cost of Biosecurity revenue 735 —

Cost of other revenue 969 —

Total $ 20,431 $ 40,782

The Company grants stock-based incentive awards pursuant to the 2021 Incentive Award Plan (the “2021 Plan”) and the 2022 Inducement Plan (the “2022 Inducement Plan”).

As of September 30, 2024, there were approximately 4.6 million shares and 0.1 million shares available for future issuance under the 2021 Plan and 2022 Inducement Plan, respectively.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

The Company grants stock-based incentive awards pursuant to the 2021 Incentive Award Plan (the “2021 Plan”) and the 2022 Inducement Plan (the “2022 Inducement Plan”).

As of March 31, 2025, there were 2,319,438 shares and 224,083 shares available for future issuance under the 2021 Plan and the 2022 Inducement Plan, respectively.

Time-based Stock Options

A summary of stock option activity for options that are subject to time-based vesting conditions for the nine months ended September 30, 2024, is presented below:

(in thousands)

A summary of stock option activity for options that are subject to time-based vesting conditions for the three months ended March 31, 2025 is presented below:

(in Thousands)

Outstanding as of December 31, 2024 267,520 $ 25.17

Granted 156 18.48

Exercised ( 102 ) 0.80

Forfeited ( 6,208 ) 92.08

Outstanding as of September 30, 2024 191 32.73 9.44 $ —

Exercisable as of September 30, 2024 34 94.75 8.25 —

Outstanding as of March 31, 2025 261,312 23.58 9.18 $ —

Exercisable as of March 31, 2025 27,339 95.35 7.75 —

(1) The aggregate intrinsic value is calculated as the difference between the Company's closing stock price on the last trading day of the quarter and the exercise prices, multiplied by the number of in-the-money stock options.

The aggregate intrinsic value of options exercised during the nine months ended September 30, 2024 and 2023 was $ 0.7 million and $ 8.4 million, respectively.

The weighted-average grant-date fair value of options granted during the nine months ended September 30, 2024 and 2023 was $ 14.14 and $ 57.20 per share, respectively, and was calculated using the following key assumptions in the Black-Scholes option-pricing model:

Nine Months Ended September 30,

Risk-free interest rate 4.24 % 3.94 %

Expected volatility 96 % 93 %

Expected term (in years) 5.7 5.5

Dividend yield — % — %

As of September 30, 2024, there was $ 1.8 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 1.6 years.

The aggregate intrinsic value of stock options exercised during the three months ended March 31, 2024 was $ 3.9 million.

There were no stock option exercises during the three months ended March 31, 2025.

As of March 31, 2025, there was $ 1.3 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 1.8 years.

Market-based Stock Options

In April 2024, the Company granted to each of the Company's four founders an option to purchase in aggregate 0.1 million shares of Ginkgo's Class A common stock with an exercise price of $ 100.00 per share, subject both to time-based and market-based vesting criteria (the “Founder Options”).

In April 2024, the Company granted to each of the Company's four founders an option to purchase in aggregate 125,000 shares of Ginkgo's Class A common stock with an exercise price of $ 100 per share, subject both to time-based and market-based vesting criteria (the “Founder Options”).

The market-based vesting is tied to the achievement of four specified stock price hurdles within a five-year period, with 10 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 200 , 10 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 300 , 20 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 400 and the remaining 60 % of the Founder Options vesting based on the achievement of a 90-calendar-day average stock price of $ 500 .

If the market-based criteria are achieved during the five-year period, the awards will vest on the five-year anniversary of the grant date.

As of March 31, 2025, there was $ 3.2 million of unrecognized compensation expense related to the market-based options recognizable over a weighted-average period of 4.1 years.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

The weighted-average grant-date fair value of the options granted was $ 7.80 per share and was calculated using a Monte Carlo simulation model with the following assumptions:

Nine Months Ended September 30, 2024

Risk-free interest rate 4.65 %

Expected volatility 71.8 %

Suboptimal exercise multiple 2.8

Dividend yield — %

As of September 30, 2024, there was $ 3.6 million of unrecognized compensation expense related to the market-based stock options recognizable over a weighted-average period of 4.6 years.

Restricted Stock Units

A summary of the restricted stock units (“RSU”) activity for the nine months ended September 30, 2024 is presented below:

(in thousands) Weighted

Restricted stock unit (“RSU”) awards granted before 2025 generally had a four-year requisite service period, with 25% of the shares vesting on the first anniversary of the grant date and the remainder vesting monthly thereafter.

RSU awards granted in March 2025 will vest in equal quarterly installments through January 2026.

A summary of the RSU activity for the three months ended March 31, 2025 is presented below:

Shares Weighted

Nonvested as of December 31, 2024 3,327,398 $ 69.00

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Forfeited ( 404,208 ) 64.01

Nonvested as of September 30, 2024 4,078 74.44

The weighted average grant date fair value of RSUs granted during the nine months ended September 30, 2024 and 2023 was $ 44.73 and $ 55.20 , respectively.

As of September 30, 2024, there was $ 241.1 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 2.8 years.

Earnout shares represent equity awards in the form of RSUs and restricted stock awards (“RSAs”) that were granted to existing shareholders of the Company as of the closing date of the Company's merger with SRNG on September 16, 2021 (the “Closing Date”).

The earnout shares are subject to the same time vesting and performance conditions (change in control or an initial public offering) as the underlying awards (including with respect to vesting and termination-related provisions).

Additionally, the earnout shares are subject to a market condition that will be met when the trading price of the Company's Class A common stock is greater than or equal to $ 500.00 , $ 600.00 , $ 700.00 and $ 800.00 for any 20 trading days within any period of 30 consecutive trading days, on or before the fifth anniversary of the Closing Date (collectively, the “Earnout Targets”).

The first Earnout Target of $ 500.00 per share was met on November 15, 2021.

Nonvested as of March 31, 2025 3,710,189 49.42

The weighted average grant date fair value of RSUs granted during the three months ended March 31, 2025 and 2024 was $ 7.95 and $ 48.40 , respectively.

As of March 31, 2025, there was $ 154.9 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 2.3 years.

Performance-based Restricted Stock Units

In March 2025, the compensation committee of the Company's board of directors approved a grant of performance-based restricted stock unit (“PSU”) awards under the 2021 Plan to substantially all employees.

The PSUs are eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2025 cash flow targets.

Recipients must remain employed through the date the applicable vested shares are distributed, which is expected to occur in March 2026.

PSU achievement percentages may range from 0% to 100%.

The grant-date fair value of the PSUs was determined based on the closing price of the Company’s Class A common stock on the grant date.

A summary of PSU activity for the three months ended March 31, 2025 is presented below:

Shares Weighted

Granted 4,148,022 $ 7.81

Forfeited ( 32,752 ) 7.81

Nonvested as of March 31, 2025 4,115,270 7.81

As of March 31, 2025, there was $ 30.4 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately one year, assuming a 100% PSU achievement rate.

Actual expense recognized may vary based on the final achievement rate.

Earnout shares represent equity awards, primarily in the form of restricted stock, granted to existing employees of the Company as of the closing date of the Company’s merger with SRNG on September 16, 2021 (the “Closing Date”).

These earnout shares are subject to the same time-based vesting and performance conditions (change in control or an initial public offering) as the underlying awards, including provisions related to vesting and termination.

Additionally, the earnout shares are subject to a market condition, which is satisfied when the trading price of the Company's common stock is greater than

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

A summary of activity during the nine months ended September 30, 2024 for the earnout shares is presented below:

(in thousands)

or equal to $ 500 , $ 600 , $ 700 and $ 800 per share for any 20 trading days within a 30 consecutive trading day period, on or before the fifth anniversary of the Closing Date (collectively, the “Earnout Targets”).

The first Earnout Target of $ 500 per share was met on November 15, 2021.

A summary of activity during the three months ended March 31, 2025 for the earnout shares is presented below:

Nonvested as of December 31, 2024 552,457 $ 510.80

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Forfeited ( 35 ) 516.11

Nonvested as of September 30, 2024 555 510.85

As of September 30, 2024, there was $ 0.4 million of unrecognized compensation expense related to earnout shares recognizable over a weighted-average period of 0.7 years.

Nonvested as of March 31, 2025 552,325 510.80

As of March 31, 2025, there was $ 0.1 million of unrecognized compensation expense related to earnout shares recognizable over a weighted-average period of 0.3 years.

Revenue Recognition

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The following table sets forth the percentage of Cell Engineering revenues by industry based on total Cell Engineering revenue:

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

Food and nutrition 64 % 24 % 39 % 17 %

Pharma and biotech 14 30 19 33

Three Months Ended March 31,

Agriculture 41 % 28 %

Pharmaceutical and biotechnology 31 28

Government and defense 16 16

Industrial and environment 7 10

Food and nutrition 4 17

Consumer and technology 1 1

Total Cell Engineering revenue 100 % 100 %

For the three months ended September 30, 2024 and 2023, the Company’s revenue from customers within the United States comprised 89 % and 81 %, respectively, of total revenue.

For the nine months ended September 30, 2024 and 2023, the Company's revenue from customers within the United States comprised 84 % and 83 %, respectively, of total revenue.

Cell Engineering revenue includes both cash and non-cash consideration.

The non-cash consideration primarily consists of equity received from customers as partial or full payment in certain contracts, which is recognized as revenue as services are provided or upon contract termination.

The Company did not receive equity as consideration for any customer contracts entered into during the three months ended March 31, 2025 and 2024, but continues to recognize non-cash revenue from prior contracts.

Cell Engineering revenue recognized relating to non-cash consideration was $ 8.7 million and $ 3.8 million for the three months ended March 31, 2025 and 2024, respectively.

The Company’s total revenue is derived from customers located primarily in the United States.

For the three months ended March 31, 2025 and 2024, the Company’s revenue from customers within the United States comprised 76 % and 70 %, respectively, of total revenue.

Contract Balances

The Company recognizes a contract asset when the Company transfers goods or services to a customer before the customer pays consideration or before payment is due, excluding any amounts presented as accounts receivable.

The Company had no contract asset balances as of September 30, 2024 and December 31, 2023.

The Company had no contract asset balances as of March 31, 2025 and December 31, 2024.

The Company’s accounts receivable consists of both billed and unbilled amounts.

Unbilled receivables arise when revenue is recognized in excess of invoiced amounts and represent the Company’s unconditional right to consideration for goods or services already transferred to the customer.

The balance of unbilled accounts receivable, included in accounts receivable, net in the accompanying condensed consolidated balance sheets, was $ 8.1 million and $ 9.1 million as of September 30, 2024 and December 31, 2023, respectively.

Contract liabilities, or deferred revenue, primarily consist of payments received in advance of performance under the contract or when the Company has an unconditional right to consideration under the terms of the contract before it transfers goods or services to the customer.

The Company’s collaborative arrangements with its investees and related parties typically include upfront payments consisting of cash or non-cash consideration for future research and development services and non-cash consideration in the form of convertible financial instruments and equity securities for licenses that

Unbilled receivables arise when revenue is recognized in excess of invoiced amounts and

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

will be transferred in the future.

represent the Company’s unconditional right to consideration for goods or services already transferred to the customer.

The balance of unbilled accounts receivable, included in accounts receivable, net in the accompanying condensed consolidated balance sheets, was $9.0 million and $11.3 million as of March 31, 2025 and December 31, 2024, respectively.

The Company records the upfront cash payments and fair value of the convertible financial instruments and equity securities as deferred revenue.

1 unchanged sentence

Contract liabilities are recognized as revenue as (or when) the Company performs under the contract.

During the nine months ended September 30, 2024, the Company recognized $ 84.3 million of revenue that was included in the contract liabilities balance of $ 202.5 million as of December 31, 2023.

During the nine months ended September 30, 2023, the Company recognized $ 59.8 million of revenue that was included in the contract liabilities balance of $ 222.6 million as of December 31, 2022.

During the three months ended March 31, 2025, the Company recognized $ 22.8 million of revenue that was included in the contract liabilities balance of $ 126.5 million as of December 31, 2024.

During the three months ended March 31, 2024, the Company recognized $ 13.8 million of revenue that was included in the contract liabilities balance of $ 202.5 million as of December 31, 2023.

Performance Obligations

The aggregate amount of the transaction price that was allocated to performance obligations that have not yet been satisfied or are partially satisfied as of September 30, 2024 and December 31, 2023 was $ 68.0 million and $ 110.0 million, respectively.

The Company has elected the practical expedient not to provide the remaining performance obligation disclosures related to contracts for which the Company recognizes revenue on a cost-plus basis in the amount to which it has the right to invoice, and for contracts with a term of one year or less.

As of September 30, 2024, of the performance obligations not yet satisfied or partially satisfied, nearly all is expected to be recognized as revenue during the years 2024 to 2029.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

The aggregate amount of the transaction price that was allocated to performance obligations that have not yet been satisfied or are partially satisfied as of March 31, 2025 and December 31, 2024 was $ 123.8 million and $ 85.8 million, respectively.

As of March 31, 2025, approximately $ 37.5 million of the unsatisfied or partially satisfied performance obligations is expected to be recognized as revenue in 2025, based on the projected customer program end date;

$ 10.3 million between 2025 and 2026;

$ 50.0 million between 2025 and 2027;

and $ 26.0 million between 2025 and 2028.

Segment Information

The Company has identified two operating and reportable segments:

The Company operates in two operating and reportable segments:

Cell Engineering and Biosecurity.

The Company’s chief operating decision makers (“CODMs”) evaluate the financial performance of the Company’s segments based upon segment revenues and operating results.

The Company’s measure of segment operating results for management reporting purposes excludes the impact of stock-based compensation expense, depreciation and amortization, asset impairment charges, restructuring charges, and change in fair value of certain contingent liabilities.

The following table presents summary results of the Company’s reportable segments for the periods indicated (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

Cell Engineering $ 75,089 $ 37,176 $ 139,183 $ 116,555

Biosecurity 13,957 18,254 44,013 100,145

Total revenue 89,046 55,430 183,196 216,700

Segment cost of revenue:

Cell Engineering 2,016 — 3,930 —

Biosecurity 9,987 6,923 30,996 47,394

Segment research and development expense:

Cell Engineering 57,201 90,889 253,790 275,494

Biosecurity 141 313 720 1,408

Total segment research and development expense 57,342 91,202 254,510 276,902

Segment general and administrative expense:

Cell Engineering 29,319 42,617 103,167 155,216

Biosecurity 10,040 12,207 33,169 42,862

Total segment general and administrative expense 39,359 54,824 136,336 198,078

Segment operating (loss) income:

This structure reflects the Company’s internal management framework and the approach its Chief Operating Decision Maker (“CODM”) uses to evaluate operating results and allocate resources.

The Company’s reportable segments are described as follows:

• Cell Engineering consists of end-to-end cell engineering solutions and cell engineering tools offerings for biological R&D.

The Company’s cell engineering platform includes two core assets:

the Foundry, a highly efficient biology laboratory powered by proprietary workflows, custom software, robotic automation, and data science and analytics, and the Codebase, a collection of biological “parts” and a database of biological data used to program cells.

The Cell Engineering segment includes costs incurred for the development, operation, expansion and enhancement of the Foundry and Codebase.

Cell Engineering revenue is generated primarily through service fees and downstream value share in the form of milestone payments, royalties or equity interests.

• Biosecurity consists of the Company’s biomonitoring and bioinformatics support services, offered to both government and non-government customers through the Company’s two core offerings:

Canopy and Horizon.

Biosecurity revenue is generated from fees for data, analytics, and services.

The Company’s reportable segments are those for which discrete financial information is available and whose results are regularly provided to the Company’s CODM, consisting of the Chief Executive Officer and the Chief Operating Officer, for the purpose of allocating resources and assessing financial performance.

The CODM evaluates the financial performance of the Company’s segments based on segment operating income (loss).

The CODM is primarily provided with the segment operating income (loss) on a quarterly basis, as well as during the annual budgeting and forecasting process, and uses this information to monitor the Company’s performance, including budget-to-actual results, and to make decisions about the allocation of operating and capital resources to each segment.

For management reporting purposes, the

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Company’s measure of segment operating income (loss) excludes the impact of stock-based compensation expense, depreciation and amortization, asset impairment charges, restructuring charges, costs associated with excess space, transaction and integration costs associated with planned, completed or terminated mergers and acquisitions, and acquired in-process research and development expenses.

The Company has determined its significant segment expenses are cost of revenue for Biosecurity, research and development expenses for Cell Engineering, and general and administrative expenses for both segments, which are regularly provided to the CODM.

The CODM is not provided with asset information by segment;

therefore, such information is not presented.

The accounting policies used to prepare the reportable segments financial information are the same as those used to prepare the Company’s consolidated financial statements.

The following table presents summary results of the Company’s reportable segments and a reconciliation of total segment operating loss to consolidated loss before income taxes (in thousands):

Three Months Ended March 31,

Cell Engineering

Biosecurity ( 6,211 ) ( 1,189 ) ( 20,872 ) 8,481

Revenue $ 38,230 $ 27,889

Costs and operating expenses:

Cost of other revenue 3,121 —

Research and development 48,670 81,898

General and administrative 18,027 38,244

Cell Engineering operating loss ( 31,588 ) ( 92,253 )

Revenue 10,088 10,055

Costs and operating expenses:

Cost of Biosecurity revenue 7,223 9,202

Research and development — 120

General and administrative 8,050 11,951

Biosecurity operating loss ( 5,185 ) ( 11,218 )

Total segment operating loss ( 36,773 ) ( 103,471 )

Operating expenses not allocated to segments:

Reconciling items to reconcile total segment operating loss to loss before income taxes:

Stock-based compensation (1)

1 unchanged sentence

Depreciation and amortization 15,366 12,869

Impairment expense (2)

— 112,403 47,858 121,404

Restructuring charges (2)

Carrying cost of excess space (net of sublease income) (3)

Merger and acquisition related expense (income) (4)

( 918 ) 2,394

Change in fair value of contingent consideration liability 1,413 1,764 3,698 10,217

Loss from operations $ ( 55,204 ) $ ( 286,393 ) $ ( 456,151 ) $ ( 686,289 )

(1) Includes $ 0.2 million and $ 1.1 million in employer payroll taxes for the three months ended September 30, 2024 and 2023, respectively, and $ 2.9 million and $ 4.3 million in employer payroll taxes for the nine months ended September 30, 2024 and 2023, respectively.

(2) For 2024, includes $ 47.9 million related to goodwill impairment.

For the three months ended September 30, 2023, includes a $ 16.2 million impairment loss on lab equipment and a $96.2 million impairment loss on an operating lease right-of-use asset and related leasehold improvements associated with an exited Zymergen leased facility.

For the nine months ended September 30, 2023, includes a $ 25.2 million impairment loss on lab equipment and a $96.2 million impairment loss on lease assets associated with the exited Zymergen leased facility.

Acquired in-process research and development — 16,871

Other (income) expense, net (5)

1,901 ( 12,122 )

Loss before income taxes $ ( 90,869 ) $ ( 165,880 )

(1) Includes $ 0.4 million and $ 1.6 million in employer payroll taxes for the three months ended March 31, 2025 and 2024, respectively.

(2) See Note 3 , Restructuring, for composition of costs.

(3) The carrying cost of excess space includes base rent, common area maintenance charges, and real estate taxes associated with facilities the Company is not occupying, net of any sublease income from these spaces.

(4) Represents transaction and integration costs directly related to mergers and acquisitions, including:

(i) legal, consulting, and accounting fees associated with acquisitions;

(ii) post-acquisition employee retention bonuses;

(iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions;

and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(5) Includes interest income, interest expense, loss on investments, changes in fair value of certain assets and liabilities, and other gains and losses.

Net Loss per Share

The Company computes net loss per share using the two-class method required for participating securities.

The earnings per share amounts are the same for the different classes of common stock because the holders of each class are legally entitled to equal per share distributions whether through dividends or liquidation.

The calculation of basic and diluted earnings per common share are as follows (in thousands, except per share amounts):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

The calculation of basic and diluted earnings per common share is as follows (in thousands, except share data):

Three Months Ended March 31,

Net loss, basic $ ( 90,957 ) $ ( 165,911 )

5 unchanged sentences

Weighted average common shares outstanding, diluted 54,241,619 50,133,366

Basic and diluted net loss per share $ ( 1.08 ) $ ( 6.21 ) $ ( 8.58 ) $ ( 14.09 )

The following potential common shares, presented based on amounts outstanding at each period end, were excluded from the calculation of diluted net loss per share for the periods presented because including them would have been anti-dilutive (in thousands):

As of September 30, 2024 As of September 30, 2023

Warrants to purchase Class A common stock (1)

51,825 51,825

Outstanding stock options 691 211

Basic net loss per share $ ( 1.68 ) $ ( 3.31 )

Diluted net loss per share $ ( 1.68 ) $ ( 3.32 )

As of March 31,

Unvested PSUs 4,115,270 —

Unvested RSUs 3,710,189 5,967,596

Earnout shares (1)

3,794,111 3,803,377

Warrants to purchase Class A common stock 1,295,622 1,295,622

Outstanding stock options 761,312 104,125

Escrow shares (2)

13,683,151 11,188,986

(1) In connection with the Company's merger with Soaring Eagle Acquisition Corp.

(“SRNG”) on September 16, 2021, the Company assumed 34.5 million formerly publicly traded warrants (“Public Warrants”) and 17.3 million private placement warrants (the “Private Placement Warrants”), initially issued in connection with SRNG’s initial public offering.

Each Warrant equals one-fortieth (1/40) of one share of Class A common stock (40 Warrants must be exercised for one share of Class A common stock).

(2) Represents earnout shares for which the service-based and/or market-based vesting conditions have not been satisfied.

(1) Represents employee and non-employee earnout shares for which the service-based and/or market-based vesting conditions have not been satisfied.

(2) Represents restricted common stock issued in connection with asset acquisitions, held in escrow for indemnification purposes, and subject to forfeiture.

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The Company’s significant transactions with its related parties are primarily comprised of revenue generating activities under collaboration and license agreements.

Significant related party transactions included in the condensed consolidated balance sheet are summarized below (in thousands):

As of September 30, 2024 As of December 31, 2023

Significant related party transactions included in the condensed consolidated balance sheet, excluding the Company’s investments and equity method investments, are summarized below (in thousands):

As of March 31, 2025 As of December 31, 2024

Deferred revenue, current and non-current:

3 unchanged sentences

Genomatica 290 564

Motif FoodWorks — 45,426

Ayana Bio 2 —

Other equity investees — 139

$ 65,177 $ 73,055

Significant related party transactions included in the condensed consolidated statement of operations and comprehensive loss are summarized below (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

Significant related party transactions included in the condensed consolidated statements of operations and comprehensive loss, excluding the losses on the Company’s investments and equity method investments, are summarized below (in thousands):

Three Months Ended March 31,

Cell Engineering revenue:

Motif FoodWorks $ 45,426 $ 6,303 $ 45,445 $ 6,306

Allonnia 391 180 77 425

Genomatica $ 274 $ 369

BiomEdit 268 632 70 2,410

Ayana Bio 240 147

Arcaea — — 4,653 5,669

Verb Biotics — 70 — 588

Allonnia 1 59

BiomEdit 7,583 —

Other equity investees — 139

$ 8,098 $ 733

Motif FoodWorks

In September 2018, the Company entered into (i) an Intellectual Property Contribution Agreement (“IPCA”) with Motif that granted Motif a license to certain of the Company’s intellectual property and (ii) a Technical Development Agreement (“TDA”) that established the terms under which the Company was to provide technical development services.

In return for the Company's contribution of intellectual property and access to its platform, the Company received shares of common stock in Motif.

The initial fair value of the common stock investment in Motif was $65.1 million, which has subsequently been reduced to a carrying value of zero as a result of the allocation of losses under the accounting for equity method investments.

The initial non-refundable fair value of the equity received, totaling $65.1 million and considered non-cash consideration under ASC 606, was accounted for as material rights under ASC 606.

The material rights pertained to Motif's license rights for a set of ingredients that the parties intended to develop within the first two years.

This amount was recorded as deferred revenue for the future license rights and recognizable as revenue as the Company performed qualifying services for Motif, or when such rights expire upon termination of the agreements.

As of December 31, 2023, the Company had a remaining

In February 2025, the Company and Motif mutually agreed to terminate Motif’s sublease of certain Company facility space whereby Motif paid the Company a termination fee of $ 1.6 million.

The termination fee was recorded as sublease income, net of certain costs.

Sublease income is recognized as a reduction of operating lease costs reported in general and administrative expenses.

In March 2025, the Company and BiomEdit mutually terminated certain agreements entered into in April 2022, which had granted BiomEdit a license to certain of the Company’s intellectual property and established the terms under which the Company would provide technical research and development services to BiomEdit.

In exchange for the Company’s contribution of intellectual property and access to its platform, the Company received shares of common stock in BiomEdit valued at $10.0 million.

The non-refundable fair value of this equity, considered non-cash consideration under ASC 606, was accounted for as material rights in accordance with ASC 606.

These material rights related to BiomEdit’s license to certain applicable patents and other intellectual property that the parties intended to develop under technical development plans.

This amount was recorded as deferred revenue for the future license rights and is recognized as revenue either as the Company performs qualifying services for BiomEdit or, if applicable, when such rights expire upon termination of the agreements.

As of December 31, 2024, the Company had a remaining deferred revenue balance of $ 7.5 million related to the material rights with BiomEdit.

As a result of the termination of certain agreements with BiomEdit, the Company no longer has any obligation to perform services for BiomEdit, and the remaining $ 7.5 million in material rights deferred revenue was recognized in full as revenue during the three months ended March 31, 2025.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

deferred revenue balance of $45.4 million with Motif under this arrangement.

Effective in August 2024, the Motif IPCA and the TDA agreements were mutually terminated with no adjustment to the original consideration.

As a result, the Company has no further obligation to perform services for Motif and, accordingly, the remaining $45.4 million in deferred revenue under this arrangement has been recognized in full as revenue in the three and nine months ended September 30, 2024.

Refer to Note 6 for additional details on the Company’s investments and equity method investments held in its related parties.

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements