What changed in this filing

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Item 1. Financial Statements

2025-08-07 compared with 2025-05-06 · 280 added, 148 removed, 562 unchanged (43% of the section changed)

3 unchanged sentences

(in thousands, except share data)

As of March 31, As of December 31,

As of June 30, 2025 As of December 31, 2024

Current assets:

31 unchanged sentences

Accumulated deficit ( 5,988,814 ) ( 5,837,557 )

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

Accumulated other comprehensive income (loss) 1,653 ( 1,806 )

Total stockholders’ equity 612,952 716,058

4 unchanged sentences

(in thousands, except share data)

Three Months Ended March 31,

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Cell Engineering revenue (1)

7 unchanged sentences

General and administrative 43,279 66,285 92,322 136,572

Goodwill impairment — 47,858 — 47,858

Restructuring charges 3,674 17,066 8,947 17,066

6 unchanged sentences

Other income (expense), net ( 896 ) ( 766 ) ( 5,185 ) 1,249

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

Total other income 4,958 5,954 3,057 18,076

Loss before income taxes ( 60,583 ) ( 216,991 ) ( 151,452 ) ( 382,871 )

Income tax expense 88 31

Income tax (benefit) expense ( 283 ) 190 ( 195 ) 221

Net loss $ ( 60,300 ) $ ( 217,181 ) $ ( 151,257 ) $ ( 383,092 )

9 unchanged sentences

Foreign currency translation adjustment 2,586 ( 172 ) 3,435 ( 3,207 )

Unrealized gains on available-for-sale securities 107 —

Unrealized gains (loss) on available-for-sale securities ( 83 ) — 24 —

Total other comprehensive (loss) income 2,503 ( 172 ) 3,459 ( 3,207 )

Comprehensive loss $ ( 57,797 ) $ ( 217,353 ) $ ( 147,798 ) $ ( 386,299 )

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

(1) Includes related party revenue of $ 420 and $ 5,146 for the three months ended June 30, 2025 and 2024, respectively, and $ 8,518 and $ 5,819 for the six months ended June 30, 2025 and 2024, respectively.

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

2 unchanged sentences

(in thousands except share data)

Three Months Ended March 31, 2024

Three Months Ended June 30, 2025

Amount Additional

3 unchanged sentences

Stockholders’

Balance as of December 31, 2023 50,032,873 $ 5 $ 6,386,191 $ ( 5,290,528 ) $ 1,484 $ 1,097,152

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

Issuance of common stock upon exercise or vesting of equity awards 624,166 — — — — —

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

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

Release of 6,647 common shares from escrow related to acquisition — — 298 — — 298

Issuance of common stock in settlement of purchase price holdback 102,922 1 776 — — 777

Stock-based compensation expense — — 22,247 — — 22,247

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

Other comprehensive income — — — — 2,503 2,503

Net loss — — — ( 60,300 ) — ( 60,300 )

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

Balance as of June 30, 2025 55,425,334 $ 6 $ 6,600,107 $ ( 5,988,814 ) $ 1,653 $ 612,952

Six Months Ended June 30, 2025

Amount Additional

6 unchanged sentences

Release of 24,913 common shares from escrow related to acquisition — — 1,237 — — 1,237

Issuance of common stock in settlement of purchase price holdback 102,922 1 776 — — 777

Stock-based compensation expense — — 42,678 — — 42,678

1 unchanged sentence

Net loss — — — ( 151,257 ) — ( 151,257 )

Balance as of June 30, 2025 55,425,334 $ 6 $ 6,600,107 $ ( 5,988,814 ) $ 1,653 $ 612,952

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 except share data)

Three Months Ended June 30, 2024

Amount Additional

Accumulated Deficit

Comprehensive

Stockholders’

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

Issuance of common stock upon exercise or vesting of equity awards 536,802 — 14 — — 14

Settlement of contingent consideration 49,301 — 2,570 — — 2,570

Issuance of common stock for asset acquisitions 473,717 — 20,925 — — 20,925

Issuance of common stock in exchange for services 68,001 — 2,500 — — 2,500

Stock-based compensation expense — — 37,146 — — 37,146

Other comprehensive loss — — — — ( 172 ) ( 172 )

Net loss — — — ( 217,181 ) — ( 217,181 )

Balance as of June 30, 2024 51,968,428 $ 5 $ 6,508,410 $ ( 5,673,620 ) $ ( 1,723 ) $ 833,072

Six Months Ended June 30, 2024

Amount Additional

Accumulated Deficit

Comprehensive

Income (Loss) Total

Stockholders’

Balance as of December 31, 2023 50,032,873 $ 5 $ 6,386,191 $ ( 5,290,528 ) $ 1,484 $ 1,097,152

Issuance of common stock upon exercise or vesting of equity awards 991,558 — 543 — — 543

Settlement of contingent consideration 73,958 — 4,447 — — 4,447

Issuance of common stock for asset acquisitions 802,038 — 36,801 — — 36,801

Issuance of common stock in exchange for services 68,001 — 2,500 — — 2,500

Stock-based compensation expense — — 77,928 — — 77,928

Other comprehensive loss — — — — ( 3,207 ) ( 3,207 )

Net loss — — — ( 383,092 ) — ( 383,092 )

Balance as of June 30, 2024 51,968,428 $ 5 $ 6,508,410 $ ( 5,673,620 ) $ ( 1,723 ) $ 833,072

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

2 unchanged sentences

(in thousands)

Three Months Ended March 31,

Six Months Ended June 30,

Cash flows from operating activities:

3 unchanged sentences

Stock-based compensation 42,678 77,928

Goodwill impairment — 47,858

Restructuring related impairment charges — 4,823

Loss on investments 3,958 9,370

6 unchanged sentences

Changes in operating assets and liabilities:

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

Accounts receivable ( 412 ) ( 1,102 )

Prepaid expenses and other current assets ( 2,272 ) 1,770

8 unchanged sentences

Purchases of marketable debt securities ( 320,132 ) —

Maturities of marketable debt securities 64,958 —

Purchases of property and equipment ( 7,660 ) ( 33,742 )

Business acquisition — ( 5,400 )

Other 262 191

Net cash used in investing activities ( 262,572 ) ( 38,951 )

29 unchanged sentences

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

Reverse Stock Split

On August 19, 2024, with the approval of our Board of Directors (the “Board of Directors”) and shareholders, the Company effected a one-for-forty (1:40) reverse stock split for our common stock.

Accordingly, all common shares presented herein relating to periods prior to this date have been retrospectively adjusted to reflect the reverse stock split.

Principles of Consolidation

8 unchanged sentences

Significant Accounting Policies

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.

Other than as noted below, there have been no new or material changes to the Company’s significant accounting policies during the six months ended June 30, 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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Marketable Securities

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

In 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.

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 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.

Unrealized gains and losses on available-for-sale marketable debt securities that are not related to credit losses are included in other comprehensive income (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.

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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 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 407,240 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 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.

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

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.

The allocation of the purchase price

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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 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.

Transaction costs associated with the Zymergen APA were not material.

Other Acquisitions

The Company completed three other asset acquisitions during the six months ended June 30, 2024.

The aggregate purchase price for the three acquisitions was $ 19.8 million and was paid with the issuance of 394,799 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 $ 3.0 million and $ 19.8 million as acquired in-process research and development expense in the accompanying condensed consolidated statements of operations and comprehensive loss for the three and six months ended June 30, 2024, respectively.

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 and commenced a restructuring plan.

In the second quarter of 2024, in connection with the Company’s plans to reduce operational expenditures, management, with the approval of the Company’s 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.

Initial workforce reductions commenced in June 2024 and continued through June 30, 2025, with further reductions expected for the remainder of 2025.

All workforce 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 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.

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

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.

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 June 30, Six Months Ended June 30,

2025 2024 2025 2024

Employee termination costs and other $ 3,674 $ 12,243 $ 8,947 $ 12,243

Impairment of right-of-use asset (1)

— 4,823 — 4,823

Total restructuring $ 3,674 $ 17,066 $ 8,947 $ 17,066

(1) Relates to a decision to sublease a certain 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.

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 (in thousands):

3 unchanged sentences

Cash payments ( 9,233 )

Liability balance at March 31, 2025 $ 4,355

Liability balance at June 30, 2025 $ 2,568

Fair Value Measurements

2 unchanged sentences

Notes to Condensed Consolidated Financial Statements

As of March 31, 2025

As of June 30, 2025

Total Level 1 Level 2 Level 3

36 unchanged sentences

Notes to Condensed Consolidated Financial Statements

(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.

(1) These securities are reported within investments on the condensed consolidated balance sheet as of December 31, 2024, and are classified as current assets as of June 30, 2025, as they are considered available for use in current operations.

(2) The fair value of Synlogic, Inc.

1 unchanged sentence

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.

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 three months ended March 31 (in thousands):

During the six months ended June 30, 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 six months ended June 30, 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 six months ended June 30, 2025 or 2024.

Notes Receivable Private Placement Warrants Contingent Consideration

3 unchanged sentences

Settlements and payments ( 50 ) — —

Conversion to preferred stock ( 1,463 ) — —

Transfers into Level 3 6,987 — —

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

Balance at June 30, 2025 $ 7,540 $ — $ 5,690

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

2 unchanged sentences

Settlements and payments — — ( 5,363 )

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

Transfers to Level 2 — ( 149 ) —

Balance at June 30, 2024 $ 13,215 $ 373 $ 21,194

Notes Receivable

1 unchanged sentence

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.

As of June 30, 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, a risk-adjusted discount rate, and a potential settlement scenario.

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

1 unchanged sentence

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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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

1 unchanged sentence

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 .

The significant unobservable (Level 3) inputs used in the fair value measurement as of June 30, 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.

During the three months ended June 30, 2025, $ 1.5 million in principal related to a convertible loan issued by a customer was converted into 10,564 shares of the entity's preferred stock, which, as a new private company investment, has been classified as an investment on the balance sheet as of June 30, 2025.

As of June 30, 2025, the Company’s notes receivable had an unpaid principal balance of $ 22.0 million and a fair value of $ 7.5 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

1 unchanged sentence

The Company also issued restricted stock in connection with acquisitions, which is subject to vesting conditions and is classified as contingent consideration liability.

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 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 Company may settle a majority of its contingent consideration liabilities in either cash or shares of Class A common stock, at its discretion, with the remainder payable in cash.

During the six months ended June 30, 2024, the Company settled $ 5.4 million of contingent consideration liabilities through a combination of $ 0.9 million in cash payments and the issuance and/or vesting of 96,763 shares of Class A common stock valued at $ 4.4 million.

No contingent consideration liabilities were settled during the six months ended June 30, 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:

March 31, 2025 December 31, 2024

June 30, 2025 December 31, 2024

Contingent Consideration Liability Valuation Technique Unobservable Input Range Range

3 unchanged sentences

Discount rate 10.6 %

During the three months ended June 30, 2025, all Dutch DNA milestones valued using the discounted cash flow method were reduced to zero due to the termination of a customer agreement to which those milestones were tied.

Nonrecurring Fair Value Measurements

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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.

1 unchanged sentence

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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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”).

During the three months ended June 30, 2024, the Company recorded a $ 4.9 million impairment loss related to its investment in Genomatica, Inc.

(“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.

During the six months ended June 30, 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 June 30, 2025, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies.

During the six months ended June 30, 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.

The Company recorded no impairment losses related to SAFEs during the three and six months ended June 30, 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

As of June 30, 2025

Amortized Cost Unrealized Gains Unrealized Losses Fair Value

7 unchanged sentences

The amortized cost and estimated fair value of marketable debt securities, including $ 85.7 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands):

As of March 31, 2025

As of June 30, 2025

Amortized cost Fair value

1 unchanged sentence

Due after one year through five years 51,642 51,706

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Investments and Equity Method Investments

2 unchanged sentences

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

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

(“Genomatica”) and Synlogic, Inc.

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

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

2 unchanged sentences

The Company accounts for its investments in Platform Ventures under the equity method.

Such investments had a carrying value of zero as of June 30, 2025 and December 31, 2024.

The Company’s marketable equity securities consist of Synlogic common stock, Synlogic warrants and the shares of common stock of other publicly traded companies.

1 unchanged sentence

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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 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.

5 unchanged sentences

Investments consisted of the following (in thousands):

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

As of June 30, 2025 As of December 31, 2024

SAFEs $ 16,689 $ 16,689

4 unchanged sentences

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

Three Months Ended March 31,

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Impairment charges $ — $ ( 4,900 ) $ ( 1,844 ) $ ( 10,112 )

1 unchanged sentence

Total loss on investments $ ( 229 ) $ ( 6,826 ) $ ( 3,922 ) $ ( 9,370 )

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

The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of June 30, 2025, including cumulative unrealized losses, were as follows (in thousands):

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of June 30, 2025

Total initial cost $ 109,460

5 unchanged sentences

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:

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.

(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 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.

As of June 30, 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.

2 unchanged sentences

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

As of March 31,

As of June 30,

Cash and cash equivalents $ 203,566 $ 730,367

3 unchanged sentences

Total cash, cash equivalents and restricted cash $ 251,351 $ 775,740

(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.

(1) Includes primarily 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.

2 unchanged sentences

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

Three Months Ended March 31,

Six Months Ended June 30,

Supplemental disclosure of non-cash investing and financing activities:

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

Purchases of property and equipment included in accounts payable and accrued expenses 35 7,936

Common stock issued as settlement of contingent consideration liability — 4,447

Common stock issued for asset acquisitions 777 18,245

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

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

Equity securities received for Cell Engineering services — 55

Property, Plant and Equipment, net

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

As of March 31, As of December 31,

As of June 30, As of December 31,

Lab equipment $ 147,892 $ 150,887

8 unchanged sentences

Property, plant and equipment, net $ 186,354 $ 203,720

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Capitalization

1 unchanged sentence

Authorized Issued Outstanding

Common stock as of March 31, 2025:

Common stock as of June 30, 2025:

Class A 10,500,000,000 46,646,454 43,822,106

7 unchanged sentences

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Intangible Assets, net

Goodwill and Intangible Assets, net

All goodwill of the Company was allocated to the Cell Engineering reporting unit and segment identified in Note 1 3 .

During the three months ended June 30, 2024, 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 three and six months ended June 30, 2024.

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

2 unchanged sentences

Amortization Period

March 31, 2025:

June 30, 2025:

Developed technology $ 111,043 $ ( 44,891 ) $ 66,152 6.9

1 unchanged sentence

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

(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):

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

During the three months ended June 30, 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 .

Amortization expense was $ 4.7 million and $ 4.9 million for the three months ended June 30, 2025 and 2024, respectively, and $ 9.4 million and $ 8.4 million for the six months ended June 30, 2025 and 2024, respectively.

As of June 30, 2025, estimated future amortization expense for identifiable intangible assets is as follows (in thousands):

Remainder of 2025 $ 9,345

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The Company does not believe any pending litigation to be material, or that the outcome of any such pending litigation, in management’s judgment based on information currently available, would have a material adverse effect on the Company’s results of operations, cash flows or financial condition.

Other Commitments

In August 2023, the Company entered into a five-year strategic cloud and AI partnership with Google Cloud, which includes minimum annual commitments to purchase cloud hosting services.

The minimum commitments may be terminated by the Company upon payment of a cancellation fee representing a percentage of the remaining purchase commitment.

If the Company is unable to negotiate a modification to the annual commitments that align with its projected requirements, material losses could be incurred.

The current annual commitment period ends on August 27, 2025 and it is unlikely that the Company will reach the minimum spend by that date and may incur a contractual liability for the shortfall of approximately $ 24.0 million on that date.

Effective April 1, 2025, the Company entered into an amendment to its four-year supply agreement with Twist for the purchase of diverse products including synthetic DNA.

The original agreement was effective as of April 1, 2022 and obligated the Company to spend a minimum of $ 58.0 million over the four-year term with the following minimum annual commitments (each annual year is defined as April 1 to March 31):

year 1, $ 10.0 million;

year 2, $ 13.0 million;

year 3, $ 16.0 million;

and year 4, $ 19.0 million.

The amendment converts the remaining minimum annual commitments into non-refundable payments creditable against future purchases by the Company, with no expiration.

The Company paid $ 4.0 million in April 2025 and is obligated to non-refundable payments of $ 5.0 million on April 1, 2026 and $ 6.0 million on April 1, 2027, respectively.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Stock-Based Compensation

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,

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Research and development $ 8,517 $ 20,066 $ 17,510 $ 43,258

3 unchanged sentences

Total $ 22,247 $ 37,146 $ 42,678 $ 77,928

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.

As of June 30, 2025, there were 2,355,001 shares and 270,627 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 three months ended March 31, 2025 is presented below:

A summary of stock option activity for options that are subject to time-based vesting conditions for the six months ended June 30, 2025 is presented below:

(in Thousands)

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

Granted 171,875 9.29

Forfeited ( 6,208 ) 92.08

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

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

Outstanding as of June 30, 2025 433,187 17.91 8.03 $ 605

Exercisable as of June 30, 2025 162,478 29.48 6.36 91

(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 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 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.

The aggregate intrinsic value of stock options exercised during the six months ended June 30, 2024 was $ 1.3 million.

There were no stock option exercises during the six months ended June 30, 2025.

The weighted-average grant-date fair value of options granted during the six months ended June 30, 2025 and 2024 was $ 7.5 and $ 14.0 per share, respectively, and was calculated using the following key assumptions in the Black-Scholes option-pricing model:

Six Months Ended June 30,

Risk-free interest rate 4.06 % 4.24 %

Expected volatility 100 % 96 %

Expected term (in years) 6.0 5.7

Dividend yield — % — %

As of June 30, 2025, there was $ 2.1 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 2.7 years.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Market-based Stock Options

The market-based vesting was 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 were achieved during the five-year period, the awards would have vested on the five-year anniversary of the grant date.

In June 2025, the compensation committee of the Company’s Board of Directors canceled the Founder Options and granted replacement performance-based restricted stock unit (“PSU”) awards (the “Founder PSU Awards”).

The cancellation and concurrent grant of replacement awards were accounted for as a modification, resulting in $ 10.5 million of incremental compensation expense.

The performance period for these awards is through December 31, 2025 and the aggregate compensation expense for the cancelled award and the new award will be recognized over the remaining requisite service period of the PSUs, which is the grant date through March 31, 2026.

The PSU awards are subject to substantially similar performance metrics, vesting terms and employment terms as described in the section “ Performance-based Restricted Stock Units ” below.

Restricted Stock Units

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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:

A summary of the RSU activity for the six months ended June 30, 2025 is presented below:

Shares Weighted

3 unchanged sentences

Forfeited ( 1,018,004 ) 57.68

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.

Nonvested as of June 30, 2025 2,496,161 49.75

The weighted average grant date fair value of RSUs granted during the six months ended June 30, 2025 and 2024 was $ 7.95 and $ 47.20 , respectively.

As of June 30, 2025, there was $ 106.8 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 2.1 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.

In March 2025, the compensation committee of the Company's Board of Directors approved a grant of 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 and bookings 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%.

PSU achievement percentages may range from 0% to 100% of the award.

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:

Additionally, as summarized above, the Founder PSU Awards were granted in June 2025.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

A summary of PSU activity for the six months ended June 30, 2025 is presented below:

Shares Weighted

1 unchanged sentence

Forfeited ( 534,104 ) 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.

Nonvested as of June 30, 2025 4,951,489 8.00

As of June 30, 2025, there was $ 34.5 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately 0.8 years, assuming a 100% PSU achievement rate.

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

1 unchanged sentence

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

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”).

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 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:

A summary of activity during the six months ended June 30, 2025 for the earnout shares is presented below:

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

1 unchanged sentence

Forfeited ( 519 ) 513.29

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.

Nonvested as of June 30, 2025 551,748 510.79

As of June 30, 2025, there was zero unrecognized compensation expense related to earnout shares.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Revenue Recognition

1 unchanged sentence

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

Three Months Ended March 31,

Agriculture 41 % 28 %

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Pharmaceutical and biotechnology 44 % 22 % 38 % 25 %

Agriculture 23 23 32 25

Government and defense 21 25 19 21

Industrial and environment 7 10

Food and nutrition 6 4 5 10

Industrial and environment 4 11 5 10

Consumer and technology 2 15 1 9

2 unchanged sentences

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.

The Company did not receive equity as consideration for any customer contracts entered into during the three and six months ended June 30, 2025 and 2024, but continues to recognize non-cash revenue from prior contracts.

Cell Engineering revenue recognized relating to non-cash consideration was $ 1.2 million and $ 8.2 million for the three months ended June 30, 2025 and 2024, respectively, and $ 9.9 million and $ 12.1 million for the six months ended June 30, 2025 and 2024, respectively.

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

For the three months ended June 30, 2025 and 2024, U.S.

customers accounted for 75 % and 84 % of total revenue, respectively.

For the six months ended June 30, 2025 and 2024, U.S.

customers accounted for 76 % and 79 %, respectively.

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 March 31, 2025 and December 31, 2024.

The Company had no contract asset balances as of June 30, 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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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.

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 $ 10.9 million and $ 11.3 million as of June 30, 2025 and December 31, 2024, 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.

3 unchanged sentences

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

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.

During the six months ended June 30, 2025, the Company recognized $ 35.6 million of revenue that was included in the contract liabilities balance of $ 126.5 million as of December 31, 2024.

During the six months ended June 30, 2024, the

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Company recognized $ 29.4 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 March 31, 2025 and December 31, 2024 was $ 123.8 million and $ 85.8 million, respectively.

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 June 30, 2025 and December 31, 2024 was $ 102.1 million and $ 85.8 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.

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;

As of June 30, 2025, approximately $ 19.0 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 dates;

$ 13.2 million between 2025 and 2026;

17 unchanged sentences

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.

For management reporting purposes, the 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.

2 unchanged sentences

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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed 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,

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Cell Engineering

15 unchanged sentences

22,526 38,226 43,326 80,623

Goodwill impairment — 47,858 — 47,858

Depreciation and amortization 15,793 17,330 31,159 30,199

Restructuring charges (2)

3,674 17,066 8,947 17,066

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

12,413 7,383 24,088 7,383

Merger and acquisition related expense (income) (4)

4 unchanged sentences

Loss before income taxes $ ( 60,583 ) $ ( 216,991 ) $ ( 151,452 ) $ ( 382,871 )

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

(1) Includes $ 0.3 million and $ 1.1 million in employer payroll taxes for the three months ended June 30, 2025 and 2024, respectively, and $ 0.6 million and $ 2.7 million in employer payroll taxes for six months ended June 30, 2025 and 2024, respectively.

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

5 unchanged sentences

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.

1 unchanged sentence

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

Three Months Ended March 31,

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Net loss, basic $ ( 60,300 ) $ ( 217,181 ) $ ( 151,257 ) $ ( 383,092 )

8 unchanged sentences

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:

As of March 31,

As of June 30,

Unvested PSUs 4,951,489 —

13 unchanged sentences

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

As of June 30, 2025 As of December 31, 2024

Deferred revenue, current and non-current:

3 unchanged sentences

Genomatica 212 564

Ayana Bio 2 —

$ 65,097 $ 73,055

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,

Three Months Ended June 30, Six Months Ended June 30,

2025 2024 2025 2024

Cell Engineering revenue:

2 unchanged sentences

Allonnia — — 1 —

Motif — — — 19

BiomEdit — — 7,583 —

Arcaea — 4,653 — 4,653

Other equity investees — — — 139

10 unchanged sentences

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.

BiomEdit is no longer

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

considered a significant related party due to a reduction of the Company’s equity ownership interest that occurred during the three months ended June 30, 2025.

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

Subsequent Events

On July 4, 2025, a budget and reconciliation package known as the One Big Beautiful Bill Act (“OBBBA”) was signed into law in the United States.

Among other provisions, the OBBBA amends U.S.

tax law including the permanent extension of certain expiring provisions of the 2017 Tax Cuts and Jobs Act, modifications to the international tax framework and the restoration of favorable tax treatment for certain business provisions.

The Company is currently evaluating the impact of the OBBBA on its consolidated financial statements.

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