What changed in this filing

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Item 1. Financial Statements

2026-05-07 compared with 2025-11-06 · 256 added, 435 removed, 452 unchanged (60% of the section changed)

3 unchanged sentences

(in thousands, except share data)

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

As of March 31, 2026 As of December 31, 2025

Current assets:

10 unchanged sentences

Other non-current assets 39,522 47,167

Assets held for sale 3,211 3,854

Total assets $ 1,033,075 $ 1,119,696

19 unchanged sentences

Accumulated deficit ( 6,232,907 ) ( 6,150,320 )

Accumulated other comprehensive income (loss) 1,996 ( 1,806 )

Accumulated other comprehensive income 1,194 1,851

Total stockholders’ equity 443,153 508,590

4 unchanged sentences

(in thousands, except share data)

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

2025 2024 2025 2024

Cell Engineering revenue (1)

Three Months Ended March 31,

$ 19,474 $ 38,230

Biosecurity revenue 9,457 13,957 30,015 44,013

Total revenue 38,837 89,046 136,759 183,196

Costs and operating expenses:

Cost of Biosecurity revenue 8,177 9,987 25,576 30,996

Cost of other revenue 3,098 4,090

1 unchanged sentence

General and administrative 37,830 39,723

Goodwill impairment — — — 47,858

Restructuring charges — 4,466

3 unchanged sentences

Interest income, net 3,596 6,081

Gain (loss) on investments 3,684 ( 6,912 ) ( 238 ) ( 16,282 )

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

Change in fair value of warrant liabilities — 1,528 — 5,701

Other income (expense), net ( 163 ) 1,572 ( 5,348 ) 2,821

Total other income (expense) 9,263 ( 1,574 ) 12,320 16,502

Loss before income taxes ( 80,754 ) ( 56,778 ) ( 232,206 ) ( 439,649 )

Loss on investments ( 1,214 ) ( 3,693 )

Other expense, net ( 7,147 ) ( 4,638 )

Total other expense ( 4,765 ) ( 2,250 )

Loss from continuing operations before income taxes ( 76,139 ) ( 83,222 )

Income tax (benefit) expense ( 80 ) 88

Net loss from continuing operations $ ( 76,059 ) $ ( 83,310 )

Net loss from discontinued operations, net of tax ( 6,528 ) ( 7,647 )

Net loss $ ( 82,587 ) $ ( 90,957 )

Net loss per share:

Basic from continuing operations $ ( 1.28 ) $ ( 1.54 )

Basic from discontinued operations ( 0.11 ) ( 0.14 )

Basic $ ( 1.39 ) $ ( 1.68 )

Diluted $ ( 1.45 ) $ ( 1.08 ) $ ( 4.22 ) $ ( 8.58 )

Weighted average common shares outstanding:

Basic 59,563,454 54,241,619

Diluted 55,633,718 52,246,129 54,916,539 51,249,902

Comprehensive loss:

2 unchanged sentences

Foreign currency translation adjustment ( 579 ) 849

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

Unrealized gains (loss) on available-for-sale securities ( 78 ) 107

1 unchanged sentence

Comprehensive loss $ ( 83,244 ) $ ( 90,001 )

(1) Includes related party revenue of zero and $ 46,659 for the three months ended September 30, 2025 and 2024, respectively, and $ 8,518 and $ 51,990 for the nine months ended September 30, 2025 and 2024, respectively.

(1) Includes related party revenue of zero and $ 8,098 for the three months ended March 31, 2026 and 2025, 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 September 30, 2025

Amount Additional

Accumulated Deficit

Comprehensive Income

Stockholders’

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

Issuance of common stock upon exercise or vesting of equity awards 435,612 — — — — —

Issuance of common stock in ATM offering, net of $ 915 issuance costs

975,300 — 9,402 — — 9,402

Stock-based compensation expense — — 17,841 — — 17,841

Other comprehensive income — — — — 343 343

Net loss — — — ( 80,755 ) — ( 80,755 )

Balance as of September 30, 2025 56,836,246 $ 6 $ 6,627,350 $ ( 6,069,569 ) $ 1,996 $ 559,783

Nine Months Ended September 30, 2025

Three Months Ended March 31, 2026

Amount Additional

5 unchanged sentences

Issuance of common stock upon exercise or vesting of equity awards 3,453,490 — — — — —

Issuance of common stock in ATM offering, net of $ 915 issuance costs

975,300 — 9,402 — — 9,402

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 — — 17,807 — — 17,807

1 unchanged sentence

Net loss — — — ( 82,587 ) — ( 82,587 )

Balance as of September 30, 2025 56,836,246 $ 6 $ 6,627,350 $ ( 6,069,569 ) $ 1,996 $ 559,783

Balance as of March 31, 2026 61,660,788 $ 6 $ 6,674,860 $ ( 6,232,907 ) $ 1,194 $ 443,153

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

2 unchanged sentences

(in thousands except share data)

Three Months Ended September 30, 2024

Amount Additional

Accumulated Deficit

Comprehensive

Income (Loss) Total

Stockholders’

Balance as of June 30, 2024 51,968,429 $ 5 $ 6,508,410 $ ( 5,673,620 ) $ ( 1,723 ) $ 833,072

Issuance of common stock upon exercise or vesting of equity awards 421,680 — — — — —

Settlement of contingent consideration 689,550 — 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 53,079,659 $ 5 $ 6,527,698 $ ( 5,730,023 ) $ 263 $ 797,943

Nine Months Ended September 30, 2024

Three Months Ended March 31, 2025

Amount Additional

5 unchanged sentences

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

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

Settlement of contingent consideration 763,508 — 9,884 — — 9,884

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

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

— — 939 — — 939

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

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

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

Other comprehensive income — — — — 956 956

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

Balance as of September 30, 2024 53,079,659 $ 5 $ 6,527,698 $ ( 5,730,023 ) $ 263 $ 797,943

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:

Net loss $ ( 232,012 ) $ ( 439,495 )

Net loss from continuing operations $ ( 76,059 ) $ ( 83,310 )

Adjustments to reconcile net loss to net cash used in operating activities:

1 unchanged sentence

Stock-based compensation 15,853 17,386

Goodwill impairment — 47,858

Restructuring related impairment charges — 4,823

Loss on investments 1,214 3,693

Loss on deconsolidation of subsidiary — 7,013

Change in fair value of notes receivable 6,759 5,285

Change in fair value of warrant liabilities — ( 5,701 )

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

Non-cash lease expense 7,114 7,379

Non-cash in-process research and development — 19,796

Accretion of discount on marketable securities ( 120 ) —

6 unchanged sentences

Accounts payable, accrued expenses and other current liabilities ( 11,601 ) 8,869

Deferred revenue, current and non-current ( 7,958 ) and ( 50,858 ) from related parties

Deferred revenue, current and non-current (includes zero and $( 7,878 ) from related parties)

( 2,606 ) ( 13,190 )

1 unchanged sentence

Other non-current liabilities ( 758 ) —

Net cash used in operating activities - continuing operations ( 46,433 ) ( 42,749 )

Net cash used in operating activities - discontinued operations ( 253 ) ( 8,772 )

Net cash used in operating activities ( 46,686 ) ( 51,521 )

3 unchanged sentences

Purchases of property and equipment ( 1,933 ) ( 7,622 )

Business acquisition — ( 5,400 )

Proceeds from sales of marketable securities — 3,951

Proceeds from sale of equipment — 591

Other 511 538

Net cash used in investing activities ( 335,388 ) ( 49,151 )

Net cash provided by (used in) investing activities 23,132 ( 198,684 )

Cash flows from financing activities:

Proceeds from ATM offering 10,317 —

Payment of issuance costs related to ATM offering ( 355 ) —

Proceeds from exercise of stock options — 84

Principal payments on finance leases ( 19 ) ( 207 )

Contingent consideration payment — ( 922 )

Other — ( 4 )

Net cash provided by (used in) financing activities 9,633 ( 1,536 )

Net cash used in financing activities ( 19 ) ( 207 )

Effect of foreign exchange rates on cash and cash equivalents ( 129 ) 74

10 unchanged sentences

Basis of Presentation and Summary of Significant Accounting Policies

The mission of Ginkgo Bioworks Holdings, Inc.

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

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.

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.

Ginkgo Bioworks Holdings, Inc.'s (“Ginkgo” or the “Company”) mission is to make biology easier to engineer.

Ginkgo sells tools and biological R&D services across a range of industries to government and commercial customers.

Ginkgo offers biological R&D services on our platform and Autonomous Lab to enable our customers to bring their products to market.

Historically, Ginkgo’s primary service offering has been cell engineering R&D services (solutions) where Ginkgo performs technical activities.

In 2024, Ginkgo expanded its service offerings to include services and lab automation equipment that provide our customers cell engineering tools for biological R&D, where Ginkgo enables its customers to conduct certain in-house R&D activities themselves.

Ginkgo's services and tools are designed to offer customers better results on the dimensions of probability of success, speed, or cost – and ideally on all three.

Our Autonomous Lab is a flexible wet lab built from our Reconfigurable Automation Cart (“RAC”) systems capable of large-scale data generation;

it powers generative AI and machine learning (“ML”) tools that enable more successful biological R&D.

Discontinued Operations

On February 26, 2026, the Company entered into a definitive agreement for the sale of its Biosecurity business, which was previously reported as a separate segment (the “Biosecurity Divestiture”).

The Biosecurity Divestiture was completed on April 3, 2026 (the “Closing Date”) whereby, Perimeter Systems, Inc.

(the “Purchaser”) issued to the Company common equity of the Purchaser representing a minority interest in the Purchaser, in exchange for substantially all of the Company’s operations comprising its Biosecurity business.

The Company and the Purchaser also entered into a transition services agreement (the “TSA”) on the Closing Date (Note 2 ).

The Company is presenting the financial results of the Biosecurity business as discontinued operations for all periods presented within the accompanying condensed consolidated statements of operations and cash flows.

The accompanying condensed consolidated balance sheets as of March 31, 2026 and December 31, 2025 reflect the transferred Biosecurity assets as held for sale.

Prior to the Biosecurity Divestiture, the Biosecurity business provided services to government customers who are working to identify, monitor, prevent, and mitigate biological threats.

Basis of Presentation

The accompanying condensed consolidated financial statements have been prepared in conformity with the rules and regulations of the Securities and Exchange Commission and generally accepted accounting principles in the United States (“GAAP”) for interim financial reporting.

The accompanying condensed consolidated financial statements have been prepared in conformity with the rules and regulations of the SEC and generally accepted accounting principles in the United States (“GAAP”) for interim financial reporting.

Accordingly, certain detailed disclosures which would normally be included with annual financial statements have been omitted.

2 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

7 unchanged sentences

All revisions to accounting estimates are recognized in the period in which the estimates are revised.

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 nine months ended September 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

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 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 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.

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.

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 OBBBA did not have a material impact on the Company’s consolidated financial statements or related disclosures.

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, 2026 as compared to the significant accounting policies described in Note 2 to the Company’s 2025 consolidated financial statements included in the 2025 Annual Report.

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 2025 consolidated financial statements included in the 2025 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”)

Discontinued Operations and Assets Held for Sale

On February 26, 2026, Ginkgo Bioworks, Inc.

(the “Seller”), a wholly owned subsidiary of the Company, entered into a Stock Purchase Agreement (the “Purchase Agreement”) with the Purchaser for the sale of its Biosecurity business, which was previously reported as a separate segment.

The Biosecurity Divestiture was completed on the Closing Date whereby the Purchaser issued to the Company shares of common equity of the Purchaser representing approximately 20 % of the issued and outstanding equity of the Purchaser on a fully diluted basis.

The common equity interest in the Purchaser constituted approximately 44 % of the outstanding common equity of the Purchaser as of the Closing Date.

The Biosecurity Divestiture is considered a strategic shift that will have a significant impact on the Company’s operations and financial results.

The Company has continuing involvement in the Biosecurity business in the form of the Company’s retained equity interest.

Accordingly, certain assets of the Biosecurity business are classified as assets held for sale on the accompanying condensed consolidated balance sheets at March 31, 2026 and December 31 2025.

The results of operations for the Biosecurity business have been classified as discontinued operations within the condensed consolidated statements of operations and cash flows for the three months ended March 31, 2026 and 2025.

The following table presents the major components of the “Loss from discontinued operations, net of tax” in the condensed consolidated statements of operations (in thousands):

Three Months Ended March 31,

Revenue $ 6,210 $ 10,088

Costs and operating expenses:

Cost of revenue 5,352 7,957

General and administrative 7,701 9,320

Restructuring charges — 807

Total operating expenses 13,053 18,084

Loss from operations ( 6,843 ) ( 7,996 )

Other income 315 349

Total other income (expense) 315 349

Loss from discontinued operations $ ( 6,528 ) $ ( 7,647 )

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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 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.

The acquisition under the Zymergen APA was accounted for as a business combination in accordance with ASC 805 and was not material to the Company’s consolidated financial statements.

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.

No goodwill or intangible assets were recognized.

Transaction costs associated with the Zymergen APA were not material.

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 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 $ 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.

The following table presents the major components of assets held for sale on the condensed consolidated balance sheets (in thousands):

As of March 31, As of December 31,

Intangible assets, net $ 2,910 $ 3,442

Property, plant and equipment, net 301 412

Total assets held for sale $ 3,211 $ 3,854

The following table presents the net cash used in discontinued operations in the condensed consolidated statements of cash flows (in thousands):

Three Months Ended March 31,

Cash flows from operating activities:

Loss from discontinued operations $ ( 6,528 ) $ ( 7,647 )

Adjustments to reconcile net loss from discontinued operations to net cash used in operating activities - discontinued operations:

Depreciation and amortization 561 544

Stock-based compensation 1,954 3,045

Changes in operating assets and liabilities:

Accounts receivable 4,242 ( 4,026 )

Prepaid expenses and other current assets 132 1,043

Accounts payable, accrued expenses and other current liabilities ( 1,934 ) ( 2,450 )

Deferred revenue, current and non-current 1,320 719

Net cash used in operating activities - discontinued operations $ ( 253 ) $ ( 8,772 )

There were no investing or financing cash flow activities for the discontinued operations in the three months ended March 31, 2026 or 2025, respectively.

The Purchase Agreement includes a TSA between the Seller and the Purchaser.

The purpose of this agreement is to ensure the continuity of business operations by having the Seller provide certain services to the Purchaser, including, but not limited to information technology access and support, certain scientific services, human resources, finance and accounting functions.

The TSA includes fixed and variable payments depending on the services used.

Services rendered pursuant to the TSA are expected to conclude within 12 months.

The billings under the TSA are not expected to be significant.

The Purchase Agreement includes a Use and Occupancy Agreement (the “U&O”) between the Seller and the Purchaser.

The U&O provides the Purchaser with access to several of the Seller's facilities for a minimum period of 12 months at agreed upon payments.

The Company will account for its equity interest in the Purchaser as an equity method investment as of the Closing Date.

The Company has no plans to dispose of its equity interest.

Restructuring

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 September 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.

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 is expected to extend into 2026 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 $ 28.0 million to $ 30.0 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.

The Company is currently unable to estimate the costs associated with consolidating its facilities.

These costs may include, but are not limited to, losses on subleases, contract terminations, asset impairments, sale or disposal of equipment or other

This plan included 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 substantially concluded by December 31, 2025.

The Company plans to consolidate certain facilities through various actions, including combining office and laboratory operations into fewer locations, subleasing unused or underutilized facilities.

While the Company has

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

long-lived assets, and related costs and fees pertaining to the consolidation, closure, or disposition of facilities.

substantially completed the majority of its facility consolidation actions with excess space available for sublease, the subleasing of unused or underutilized facilities is expected to extend throughout 2026 and may not occur prior to termination of such lease, depending on market conditions.

The Company is currently unable to estimate the costs associated with consolidating its facilities.

These costs may include, but are not limited to, losses on subleases, contract terminations, asset impairments, sale or disposal of equipment or other long-lived assets, and related costs and fees pertaining to the consolidation, closure, or disposition of facilities.

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

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, Nine Months Ended September 30,

2025 2024 2025 2024

Employee termination costs and other $ 1,745 $ 2,949 $ 10,692 $ 15,192

Impairment of right-of-use asset (1)

Total restructuring $ 1,745 $ 2,949 $ 10,692 $ 20,015

(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 sheets (in thousands):

1 unchanged sentence

Liability balance at December 31, 2025 $ 2,601

Expenses incurred 10,692

Cash payments ( 2,601 )

Liability balance at September 30, 2025 $ 2,782

Liability balance at March 31, 2026 $ —

Restructuring charges were $ 4.5 million during the three months ended March 31, 2025, consisting entirely of employee termination costs and other.

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):

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of September 30, 2025

As of March 31, 2026

Total Level 1 Level 2 Level 3

1 unchanged sentence

Money market funds $ 116,715 $ 116,715 $ — $ —

Commercial paper 7,666 — 7,666 —

Treasury securities 7,977 7,977 — —

4 unchanged sentences

Marketable equity securities 17,803 17,803 — —

19,718 19,718 — —

Synlogic, Inc.

Marketable equity securities 1,286 1,286 — —

Other non-current assets:

Notes receivable 7,126 — — 7,126

Total assets $ 355,674 $ 272,981 $ 82,693 $ —

4 unchanged sentences

Total liabilities $ 5,690 $ — $ — $ 5,690

As of December 31, 2024

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

December 31, 2025

Total Level 1 Level 2 Level 3

1 unchanged sentence

Money market funds $ 146,136 $ 146,136 $ — $ —

Marketable securities:

Commercial paper 4,060 — 4,060 —

Treasury securities 118,038 118,038 — —

Corporate bonds 114,666 — 114,666 —

Marketable equity securities 18,654 18,654 — —

Synlogic, Inc.

8 unchanged sentences

Total liabilities $ 5,690 $ — $ — $ 5,690

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(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 September 30, 2025, as they are considered available for use in current operations.

(1) 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 nine months ended September 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 nine months ended September 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 nine months ended September 30, 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 nine months ended September 30 (in thousands):

Notes Receivable Private Placement Warrants Contingent Consideration

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.

There were no other transfers between Levels 1, 2, or 3 during the three months ended March 31, 2026 or 2025.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Notes Receivable Contingent Consideration

Balance at January 1, 2026 $ 7,126 $ 5,690

2 unchanged sentences

Settlements and payments — —

Conversion to preferred stock ( 1,463 ) — —

Transfers into Level 3 6,987 — —

Balance at September 30, 2025 $ 7,126 $ — $ 5,690

Balance at March 31, 2026 $ — $ 5,690

Balance at January 1, 2025 $ 1,843 $ 9,922

2 unchanged sentences

Settlements and payments ( 50 ) —

Transfers to Level 2 — ( 149 ) —

Conversion to common stock ( 10,476 ) — —

Balance at September 30, 2024 $ 3,171 $ — $ 15,263

Transfers into Level 3 6,983 —

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

Notes Receivable

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 September 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.

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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

For all of its notes receivable, the Company has elected the fair value option, under which changes in fair value are recorded in other 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.

(“Bolt”), 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.

During the three months ended March 31, 2026, Bolt disclosed it ceased operations.

Any proceeds recovered from the Bolt note as the result of a potential disposition of Bolt assets are expected to be immaterial.

As such, during the three months ended March 31, 2026, the Company reduced the carrying value of the senior secured note to zero.

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

The Company also held 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 September 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 .

The significant unobservable (Level 3) inputs used in the fair value measurement as of December 31, 2025 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.

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 September 30, 2025.

As of September 30, 2025, the Company’s notes receivable had an unpaid principal balance of $ 22.0 million and a fair value of $ 7.1 million, compared to an unpaid principal balance of $ 25.1 million and a fair value of $ 14.2 million as of December 31, 2024.

As of March 31, 2026, the Company’s convertible notes receivable had an unpaid principal balance of $ 7.5 million and a fair value of zero , compared to an unpaid principal balance of $ 9.7 million and a fair value of $ 0.5 million as of December 31, 2025.

Contingent Consideration

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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 nine months ended September 30, 2024, the Company settled $ 12.7 million of contingent consideration liabilities through a combination of $ 2.8 million in cash payments and the issuance and/or vesting of 786,313 shares of Class A common stock valued at $ 9.9 million.

No contingent consideration liabilities were settled during the nine months ended September 30, 2025.

No contingent consideration liabilities were settled during the three months ended March 31, 2026 or 2025, respectively.

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, 2025 December 31, 2024

March 31, 2026 December 31, 2025

Contingent Consideration Liability Valuation Technique Unobservable Input Range Range

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Discount rate 15.7 %

Earnout payments (Dutch DNA acquisition) Discounted cash flow Projected years of payments 2028 - 2031

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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Nonrecurring Fair Value Measurements

2 unchanged sentences

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

During the three and nine months ended September 30, 2025, the Company recorded a $ 2.7 million downward adjustment from an observable price change related to one of its investments in non-marketable equity securities.

During the nine months ended September 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.

The Company recorded no impairment losses related to SAFEs during the three and nine months ended September 30, 2025 .

During the three months ended March 31, 2026, the Company recorded no impairment losses related to its investments in the preferred stock of privately held companies.

During the three months ended March 31, 2025, the Company recorded an impairment 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.

No impairment losses related to Simple Agreements for Future Equity (“SAFEs”) were recorded during the three months ended March 31, 2026 or 2025, respectively.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Marketable Securities

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

As of September 30, 2025

As of March 31, 2026

Amortized Cost Unrealized Gains Unrealized Losses Fair Value

6 unchanged sentences

Marketable securities $ 211,741 $ 111 $ ( 63 ) $ 229,592

The amortized cost and estimated fair value of marketable debt securities, including $ 33.6 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands):

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of September 30, 2025

December 31, 2025

Amortized Cost Unrealized Gains Unrealized Losses Fair Value

Treasury securities $ 117,919 $ 171 ( 52 ) 118,038

Corporate bonds 114,640 147 ( 121 ) 114,666

Commercial paper 4,079 — ( 19 ) 4,060

Marketable equity securities — — — 18,654

Total marketable securities 236,638 318 ( 192 ) 255,418

cash equivalents — — — —

Marketable securities $ 236,638 $ 318 $ ( 192 ) $ 255,418

The amortized cost and estimated fair value of marketable debt securities at March 31, 2026, including $ 8.0 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands):

Amortized cost Fair value

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

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

Such investments had a carrying value of zero as of March 31, 2026 and December 31, 2025.

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

Marketable equity securities are measured at fair value with changes in fair value recorded in other income (expense) in the condensed consolidated statements of operations and comprehensive loss.

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.

The Company’s non-marketable equity securities

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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.

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Investments consisted of the following (in thousands):

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

As of March 31, 2026 As of December 31, 2025

SAFEs $ 2,188 $ 2,188

3 unchanged sentences

Total $ 14,703 $ 15,066

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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

2025 2024 2025 2024

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

Three Months Ended March 31,

Impairment charges $ — $ ( 1,844 )

Unrealized gains (losses) recognized on marketable equity securities and warrants 6,397 ( 6,912 ) 4,319 ( 6,170 )

Downward adjustments from observable price changes ( 2,713 ) — ( 2,713 ) —

Total gain (loss) on investments $ 3,684 $ ( 6,912 ) $ ( 238 ) $ ( 16,282 )

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

As of September 30, 2025

Unrealized losses recognized on marketable equity securities and warrants ( 1,214 ) ( 1,849 )

Total loss on investments $ ( 1,214 ) $ ( 3,693 )

The carrying value of non-marketable equity securities accounted for using the fair value measurement alternative and still held as of March 31, 2026, including cumulative unrealized losses, were as follows (in thousands):

As of March 31, 2026

Total initial cost $ 109,460

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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:

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

not the primary beneficiary of these entities because:

(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.

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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, 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 March 31, 2026 and December 31, 2025, 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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Supplemental Financial Information

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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 September 30,

As of March 31,

Cash and cash equivalents $ 143,864 $ 312,420

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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

Purchases of property and equipment included in accounts payable and accrued expenses $ 179 $ 96

Common stock issued as settlement of contingent consideration liability — 9,884

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

Conversion of notes receivable for common stock — 10,476

Issuance costs related to ATM offering included in accounts payable and accrued expenses 560 —

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 September 30, As of December 31,

As of March 31, As of December 31,

Lab equipment $ 140,681 $ 143,182

8 unchanged sentences

Property, plant and equipment, net $ 163,020 $ 167,371

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Capitalization

1 unchanged sentence

Authorized Issued Outstanding

Common stock as of September 30, 2025:

Common stock as of March 31, 2026:

Class A 10,500,000,000 53,159,223 50,254,065

7 unchanged sentences

15,800,000,000 61,680,449 58,207,298

At-The-Market Program

On September 4, 2025, the Company entered into a Sales Agreement (the “Sales Agreement”) with Allen & Company LLC (“Allen”), who is acting as the sales agent (the “Agent”), pursuant to which the Company may sell shares of its Class A common stock from time to time at prices and on terms determined by market conditions at the time of offering, up to an aggregate offering price of $ 100.0 million (the “Shares”) through or directly to the Agent in one or more at-the-market (“ATM”) offerings.

Since inception of the Sales Agreement through September 30, 2025, the Company has issued 975,300 shares of Class A common stock under the ATM Sales Agreement for net proceeds of $ 9.4 million.

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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.

At-The-Market Program

On September 4, 2025, the Company entered into a Sales Agreement (the “Sales Agreement”) with Allen & Company LLC (“Allen”), who is acting as the sales agent (the “Agent”), pursuant to which the Company may sell shares of its Class A common stock from time to time at prices and on terms determined by market conditions at the time of offering, up to an aggregate offering price of $ 100.0 million through or directly to the Agent in one or more at-the-market (“ATM”) offerings.

Since inception of the Sales Agreement through March 31, 2026, the Company has issued 1.9 million shares of Class A common stock under the Sales Agreement for net proceeds of $ 18.1 million.

Intangible Assets, net

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

2 unchanged sentences

Amortization Period

September 30, 2025:

March 31, 2026:

Developed technology $ 99,928 $ ( 51,068 ) $ 48,860 7.3

2 unchanged sentences

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

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 $ 4.6 million and $ 4.9 million for the three months ended September 30, 2025 and 2024, respectively, and $ 14.0 million and $ 13.3 million for the nine months ended September 30, 2025 and 2024, respectively.

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

Amortization expense was $ 4.2 million and $ 4.2 million for the three months ended March 31, 2026 and 2025, respectively.

As of March 31, 2026, estimated future amortization expense for identifiable intangible assets is as follows (in thousands):

Remainder of 2026 $ 12,402

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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 included minimum annual commitments to purchase cloud hosting services.

The partnership previously included minimum

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

annual commitments over the contract years ending August 27 to purchase cloud hosting services in exchange for various discounts on such services.

The minimum annual commitments were as follows:

year 1, $ 8.0 million;

year 2, $ 28.0 million;

year 3, $ 54.0 million;

year 4, $ 86.0 million;

and year 5, $ 113.0 million.

As of August 27, 2025, the end of the second commitment period, the Company had incurred a $ 21.4 million shortfall.

A liability for that amount is recorded in Accrued expenses and other current liabilities in the accompanying condensed consolidated balance sheets as of September 30, 2025.

Effective October 3, 2025, the Company entered into amendment that revised and reset the annual commitments as follows (each annual year is defined as October 3 to October 2):

year 1 (starting on October 3, 2025), $ 6.0 million;

year 2, $ 8.0 million;

year 3, $ 12.0 million;

year 4, $ 18.0 million;

year 5, $ 28.0 million;

year 6, $ 38.0 million.

Additionally, in the fourth quarter of 2025, the Company is required to make a one-time payment of $ 14.0 million to be released from its minimum annual commitment obligations under the original agreement.

If the Company does not meet its minimum annual commitment obligations in the future, additional shortfall liabilities may be incurred.

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.

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 September 30, Nine Months Ended September 30,

2025 2024 2025 2024

Three Months Ended March 31,

Research and development $ 8,023 $ 8,993

General and administrative 7,403 7,424

Cost of Biosecurity revenue 534 — 2,127 —

Cost of other revenue 427 969

1 unchanged sentence

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, 2025, there were 2,911,242 shares and 289,240 shares available for future issuance under the 2021 Plan and the 2022 Inducement Plan, respectively.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of March 31, 2026, there were 3,625,465 shares and 292,639 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, 2025 is presented below:

A summary of stock option activity for options that are subject to time-based vesting conditions for the three months ended March 31, 2026 is presented below:

(in Thousands)

Outstanding as of December 31, 2025 366,567 $ 15.38

Granted 171,875 9.29

Forfeited — —

Outstanding as of September 30, 2025 366,567 15.38 9.20 $ 1,481

Exercisable as of September 30, 2025 115,934 27.59 8.58 194

Outstanding as of March 31, 2026 366,567 15.38 8.70 $ —

Exercisable as of March 31, 2026 136,014 24.74 8.16 —

(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 nine months ended September 30, 2024 was $ 0.7 million.

There were no stock option exercises during the nine months ended September 30, 2025.

The weighted-average grant-date fair value of options granted during the nine months ended September 30, 2025 and 2024 was $ 7.50 and $ 14.14 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 4.06 % 4.24 %

Expected volatility 100 % 96 %

Expected term (in years) 6.0 5.7

Dividend yield — % — %

As of September 30, 2025, there was $ 1.7 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 2.5 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 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.

There were no stock option exercises during the three months ended March 31, 2026 and 2025, respectively.

As of March 31, 2026, there was $ 1.3 million of unrecognized compensation expense related to time-based stock options recognizable over a weighted-average period of 2.0 years.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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

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 nine months ended September 30, 2025 is presented below:

RSU awards granted in March 2026 and after will vest in equal quarterly installments through January 2027.

A summary of the RSU activity for the three months ended March 31, 2026 is presented below:

Shares Weighted

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Forfeited ( 129,381 ) 48.45

Nonvested as of September 30, 2025 1,850,409 50.41

The weighted average grant date fair value of RSUs granted during the nine months ended September 30, 2025 and 2024 was $ 7.99 and $ 44.73 , respectively.

As of September 30, 2025, there was $ 79.8 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 2.0 years.

Nonvested as of March 31, 2026 1,378,406 39.87

The weighted average grant date fair value of RSUs granted during the three months ended March 31, 2026 and 2025 was $ 7.05 and $ 7.95 , respectively.

As of March 31, 2026, there was $ 46.6 million of unrecognized compensation expense related to RSUs recognizable over a weighted-average period of 1.6 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 were eligible to vest based on the achievement of specific performance metrics tied to the Company’s 2025 cash flow and bookings targets.

PSU achievement percentages ranged from 49 % 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.

In March 2026, the compensation committee of the Company's Board of Directors approved a grant of PSU awards under the 2021 Plan to substantially all employees.

1 unchanged sentence

Recipients must remain employed through the date the applicable vested shares are distributed, which is expected to occur in March 2027.

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

PSU achievement percentages may range from zero 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.

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 nine months ended September 30, 2025 is presented below:

A summary of PSU activity for the three months ended March 31, 2026 is presented below:

Shares Weighted

Granted 5,493,893 $ 7.98

Forfeited ( 840,064 ) 7.81

Nonvested as of September 30, 2025 4,653,829 8.01

As of September 30, 2025, there was $ 28.0 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately 0.5 years, 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 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 nine months ended September 30, 2025 for the earnout shares is presented below:

Nonvested as of December 31, 2025 4,407,287 $ 8.06

Granted 3,078,611 6.38

Vested ( 3,107,417 ) 8.04

Forfeited ( 1,362,346 ) 8.05

Nonvested as of September 30, 2025 551,277 510.78

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

Nonvested as of March 31, 2026 3,016,135 7.05

As of March 31, 2026, there was $ 20.0 million of unrecognized compensation expense related to unvested PSUs outstanding, which is expected to be recognized over a service period of approximately 1.0 year, assuming a 100% PSU achievement rate.

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

(“SRNG”) on September 16, 2021 (the “SRNG Closing Date”).

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 SRNG Closing Date (collectively, the “Earnout Targets”).

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

No earnout shares vested or were forfeited during the three months ended March 31, 2026.

As of March 31, 2026, there were 551,277 nonvested earnout shares with a weighted average grant date fair value of $ 510.78 .

As of March 31, 2026, there was zero unrecognized compensation expense related to earnout shares.

Revenue Recognition

Disaggregation of Revenue

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,

2025 2024 2025 2024

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

Three Months Ended March 31,

Pharmaceutical and biotechnology 38 % 31 %

Agriculture 29 11 31 18

Government and defense 35 16

Agriculture 13 41

Food and nutrition 7 4

1 unchanged sentence

Consumer and technology — 1

Total Cell Engineering revenue 100 % 100 % 100 % 100 %

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

Total revenue 100 % 100 %

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 and nine months ended September 30, 2025 and 2024, but continues to recognize non-cash revenue from prior contracts.

Cell Engineering revenue recognized relating to non-cash consideration was zero and $ 48.0 million for the three months ended September 30, 2025 and 2024, respectively, and $ 9.9 million and $ 60.1 million for the nine months ended September 30, 2025 and 2024, respectively.

The Company did not receive equity as consideration for any customer contracts entered into during the three months ended March 31, 2026 and 2025, but continues to recognize non-cash revenue from prior contracts.

Revenue recognized relating to non-cash consideration was $ 0.5 million and $ 8.7 million for the three months ended March 31, 2026 and 2025, respectively.

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

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

customers accounted for 76 % and 89 % of total revenue, respectively.

For the nine months ended September 30, 2025 and 2024, U.S.

For the three months ended March 31, 2026 and 2025, U.S.

customers accounted for 66 % and 81 %, respectively.

For the three months ended March 31, 2026 and 2025, customers from Denmark accounted for 13 % and 11 %, 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 September 30, 2025 and December 31, 2024.

The Company had no contract asset balances as of March 31, 2026 and December 31, 2025.

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 $ 11.2 million and $ 11.3 million as of September 30, 2025 and December 31, 2024, respectively.

The balance of unbilled accounts receivable, included in accounts receivable, net in the accompanying condensed consolidated balance sheets, was $ 11.4 million and $ 14.5 million as of March 31, 2026 and December 31, 2025, respectively.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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.

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

During the nine months ended September 30, 2025, the Company recognized $ 41.4 million of revenue that was included in the contract liabilities balance of $ 126.5 million as of December 31, 2024.

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 three months ended March 31, 2026, the Company recognized $ 9.2 million of revenue that was included in the contract liabilities balance of $ 94.1 million as of December 31, 2025.

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.

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, 2025 and December 31, 2024 was $ 81.3 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 March 31, 2026 and December 31, 2025 was $ 127.4 million and $ 136.8 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 September 30, 2025, approximately $ 5.6 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;

As of March 31, 2026, approximately $ 15.8 million of the unsatisfied or partially satisfied performance obligations is expected to be recognized as revenue in 2026, based on the projected customer program end dates;

$ 40.8 million between 2026 and 2027;

$ 63.2 million between 2026 and 2028;

$ 3.4 million between 2026 and 2029;

and $ 4.2 million between 2026 and 2030.

Segment Information

The Company operates in two operating and reportable segments:

Cell Engineering and Biosecurity.

As a result of the Biosecurity Divestiture (Note 2 ), the Company manages its operations as a single operating and reportable segment.

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 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;

The Company’s reportable segment is that 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 President, for the purpose of allocating resources and assessing financial performance.

The CODM evaluates the financial performance of the Company’s segment based on loss from continuing operations before income taxes.

The CODM is primarily provided with the loss from continuing operations before income taxes 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.

The Company has determined its significant segment expenses are cost of revenue, research and development expenses, and general and administrative expenses (exclusive of certain costs and expenses), which are regularly provided to the CODM.

The CODM is not provided with asset information;

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 classification of costs differs from the presentation in the condensed consolidated statement of operations as described below.

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 September 30, Nine Months Ended September 30,

2025 2024 2025 2024

Cell Engineering

The following table presents summary results of the Company’s reportable segment, including significant expenses, and a reconciliation to loss from continuing operations before income taxes (in thousands):

Three Months Ended March 31,

Revenue $ 19,474 $ 38,230

2 unchanged sentences

Research and development (1)

General and administrative 12,170 23,088 44,338 94,534

Cell Engineering operating loss ( 36,738 ) ( 5,152 ) ( 78,263 ) ( 180,429 )

Revenue 9,457 13,957 30,015 44,013

Costs and operating expenses:

Cost of Biosecurity revenue 7,643 9,987 23,449 30,996

Research and development — 141 — 720

30,105 48,670

General and administrative (1)

Biosecurity operating loss ( 4,878 ) ( 6,211 ) ( 14,877 ) ( 20,872 )

Total segment operating loss ( 41,616 ) ( 11,363 ) ( 93,140 ) ( 201,301 )

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

12,723 19,654

Stock-based compensation (2)

16,708 17,713

Goodwill impairment — — — 47,858

Depreciation and amortization 12,799 14,822

Restructuring charges (3)

1,745 2,948 10,692 20,015

Carrying cost of excess space (net of sublease income) (4)

1 unchanged sentence

Merger and acquisition related expense (income) (5)

57 ( 796 ) ( 4,478 ) 6,110

Acquired in-process research and development — — — 19,849

Other (income) expense, net (6)

( 9,263 ) 2,805 ( 12,320 ) ( 14,145 )

Loss before income taxes $ ( 80,754 ) $ ( 56,778 ) $ ( 232,206 ) $ ( 439,649 )

(1) Includes $ 0.3 million and $ 0.2 million in employer payroll taxes for the three months ended September 30, 2025 and 2024, respectively, and $ 0.9 million and $ 2.9 million in employer payroll taxes for nine months ended September 30, 2025 and 2024, respectively.

Loss from continuing operations before income taxes $ ( 76,139 ) $ ( 83,222 )

(1) The costs and operating expenses exclude expenses which are separately captioned below.

(2) Includes $ 0.9 million and $ 0.4 million in employer payroll taxes for three months ended March 31, 2026 and 2025, respectively.

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

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(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.

and (iv) securities litigation costs.

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Net Loss per Share

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

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

2025 2024 2025 2024

Net loss, basic $ ( 80,755 ) $ ( 56,403 ) $ ( 232,012 ) $ ( 439,495 )

Change in fair value of contingent consideration common shares liability — 29 — 331

Net loss, diluted $ ( 80,755 ) $ ( 56,432 ) $ ( 232,012 ) $ ( 439,826 )

Weighted average common shares outstanding, basic 55,633,718 52,240,559 54,916,539 51,244,332

Effect of dilutive securities:

Contingent consideration common shares — 5,570 — 5,570

Weighted average common shares outstanding, diluted 55,633,718 52,246,129 54,916,539 51,249,902

Basic net loss per share $ ( 1.45 ) $ ( 1.08 ) $ ( 4.22 ) $ ( 8.58 )

Diluted net loss per share $ ( 1.45 ) $ ( 1.08 ) $ ( 4.22 ) $ ( 8.58 )

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 September 30,

As of March 31,

Unvested PSUs 3,016,135 4,115,270

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 September 30, 2025 As of December 31, 2024

As of March 31, 2026 As of December 31, 2025

Deferred revenue, current and non-current:

1 unchanged sentence

Arcaea 28,413 28,413

BiomEdit — 7,583

Genomatica 212 564

$ 64,908 $ 64,908

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 September 30, Nine Months Ended September 30,

2025 2024 2025 2024

Cell Engineering revenue:

Three Months Ended March 31,

Genomatica $ 274

Ayana Bio 240

Allonnia — 391 1 77

Motif — 45,426 — 45,445

BiomEdit 7,583

Arcaea — — — 4,653

Other equity investees — — — 139

$ — $ 46,659 $ 8,518 $ 51,990

During the three months ended March 31, 2026, the Company recognized zero revenue from related parties.

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.

6 unchanged sentences

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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

revenue was recognized in full as revenue during the three months ended March 31, 2025.

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 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.

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Subsequent Events

Refer to Note 2 for a description of the Biosecurity Divestiture, which closed subsequent to March 31, 2026.

Additionally, in April 2026, the Company was required to restrict $ 47.0 million of cash and cash equivalents to secure a surety bond of the same amount to fulfill its obligations under a contract with a U.S.

Government National Laboratory related to the sale of RAC automation equipment.

The $ 47.0 million will remain restricted until the Company completes all of its obligations under the contract.

Currently the Company expects the cash to be restricted until 2029.

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