What changed in this filing

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Item 1. Financial Statements

2025-11-06 compared with 2025-08-07 · 193 added, 148 removed, 694 unchanged (33% of the section changed)

3 unchanged sentences

(in thousands, except share data)

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

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

Current assets:

38 unchanged sentences

(in thousands, except share data)

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

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

2025 2024 2025 2024

14 unchanged sentences

Interest income, net 5,742 9,251 17,906 31,275

Loss on investments ( 229 ) ( 6,826 ) ( 3,922 ) ( 9,370 )

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 4,958 5,954 3,057 18,076

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

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

11 unchanged sentences

Foreign currency translation adjustment 27 494 3,462 ( 2,713 )

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

Unrealized gains (loss) on available-for-sale securities 316 — 340 —

1 unchanged sentence

Comprehensive loss $ ( 80,412 ) $ ( 54,417 ) $ ( 228,210 ) $ ( 440,716 )

(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.

(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.

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

2 unchanged sentences

(in thousands except share data)

Three Months Ended June 30, 2025

Three Months Ended September 30, 2025

Amount Additional

Accumulated Deficit

Comprehensive

(Loss) Income

Comprehensive Income

Stockholders’

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

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 — — — — —

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

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

1 unchanged sentence

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

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

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

Amount Additional

1 unchanged sentence

Comprehensive

(Loss) Income Total

Income (Loss) Total

Stockholders’

1 unchanged sentence

Issuance of common stock upon exercise or vesting of equity awards 1,392,239 — — — — —

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

2 unchanged sentences

Net loss — — — ( 232,012 ) — ( 232,012 )

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

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

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

2 unchanged sentences

(in thousands except share data)

Three Months Ended June 30, 2024

Three Months Ended September 30, 2024

Amount Additional

1 unchanged sentence

Comprehensive

Income (Loss) Total

Stockholders’

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

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

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

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

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

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

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

Six Months Ended June 30, 2024

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

Amount Additional

5 unchanged sentences

Issuance of common stock upon exercise or vesting of equity awards 1,413,239 — 543 — — 543

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

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

2 unchanged sentences

Stock-based compensation expense — — 91,783 — — 91,783

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

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

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

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

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

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

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

2 unchanged sentences

(in thousands)

Six Months Ended June 30,

Nine Months Ended September 30,

Cash flows from operating activities:

6 unchanged sentences

Loss on investments 275 16,282

Loss on deconsolidation of subsidiary — 7,013

Change in fair value of notes receivable 5,685 —

3 unchanged sentences

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

Accretion of discount on marketable securities ( 2,502 ) —

Other non-cash activity 1,611 655

6 unchanged sentences

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

( 27,209 ) ( 67,779 )

Operating lease liabilities, current and non-current ( 18,793 ) ( 11,383 )

6 unchanged sentences

Business acquisition — ( 5,400 )

Proceeds from sales of marketable securities — 3,951

Proceeds from sale of equipment — 591

Other 511 538

1 unchanged sentence

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

1 unchanged sentence

Contingent consideration payment — ( 922 )

Net cash used in financing activities ( 305 ) ( 1,071 )

Other — ( 4 )

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

Effect of foreign exchange rates on cash and cash equivalents 353 ( 208 )

36 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 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.

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.

14 unchanged sentences

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.

Recently Issued Accounting Pronouncements

5 unchanged sentences

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.

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.

3 unchanged sentences

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

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.

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.

1 unchanged sentence

Other Acquisitions

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

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.

1 unchanged sentence

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.

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.

Restructuring

1 unchanged sentence

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 June 30, 2025, with further reductions expected for the remainder of 2025.

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 may extend beyond 2025 or may not occur prior to termination of such lease, depending on market conditions.

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.

2 unchanged sentences

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.

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

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.

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 June 30, Six Months Ended June 30,

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

2025 2024 2025 2024

1 unchanged sentence

Impairment of right-of-use asset (1)

— 4,823 — 4,823

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 sheet (in thousands):

Employee Termination Costs and Other

2 unchanged sentences

Cash payments ( 10,764 )

Liability balance at June 30, 2025 $ 2,568

Liability balance at September 30, 2025 $ 2,782

Fair Value Measurements

2 unchanged sentences

Notes to Condensed Consolidated Financial Statements

As of June 30, 2025

As of September 30, 2025

Total Level 1 Level 2 Level 3

3 unchanged sentences

Treasury securities 25,956 25,956 — —

Corporate bonds 10,874 — 10,874 —

Marketable securities:

30 unchanged sentences

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 June 30, 2025, as they are considered 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 September 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 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.

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 six months ended June 30 (in thousands):

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.

Notes Receivable Private Placement Warrants Contingent Consideration

5 unchanged sentences

Transfers into Level 3 6,987 — —

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

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

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

3 unchanged sentences

Transfers to Level 2 — ( 149 ) —

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

Conversion to common stock ( 10,476 ) — —

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

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 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.

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 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

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

within the fair value hierarchy.

applicable market yield or discount rate.

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

2 unchanged sentences

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 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 .

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 .

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 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.

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.

Contingent Consideration

2 unchanged sentences

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.

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.

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.

3 unchanged sentences

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:

June 30, 2025 December 31, 2024

September 30, 2025 December 31, 2024

Contingent Consideration Liability Valuation Technique Unobservable Input Range Range

4 unchanged sentences

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

Nonrecurring Fair Value Measurements

The Company measures the fair value of certain assets, including investments in privately held companies without readily determinable fair values, on a nonrecurring basis when events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable 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.

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

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.

2 unchanged sentences

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”).

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 six months ended June 30, 2025

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

Marketable Securities

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

As of June 30, 2025

As of September 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 $ 33.6 million classified in cash and cash equivalents, are summarized below by contractual maturity dates (in thousands):

As of June 30, 2025

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

As of September 30, 2025

Amortized cost Fair value

1 unchanged sentence

Due after one year through five years 27,019 27,088

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

Investments and Equity Method Investments

7 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.

Such investments had a carrying value of zero as of September 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.

9 unchanged sentences

Investments consisted of the following (in thousands):

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

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

SAFEs $ 16,689 $ 16,689

3 unchanged sentences

Total $ 30,175 $ 48,704

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

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

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

1 unchanged sentence

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

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 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

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

Total initial cost $ 109,460

8 unchanged sentences

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 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.

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.

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

1 unchanged sentence

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 June 30,

As of September 30,

Cash and cash equivalents $ 111,065 $ 616,214

8 unchanged sentences

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

Six Months Ended June 30,

Nine Months Ended September 30,

Supplemental disclosure of non-cash investing and financing activities:

5 unchanged sentences

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

1 unchanged sentence

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

As of June 30, As of December 31,

As of September 30, As of December 31,

Lab equipment $ 146,639 $ 150,887

13 unchanged sentences

Authorized Issued Outstanding

Common stock as of June 30, 2025:

Common stock as of September 30, 2025:

Class A 10,500,000,000 48,170,140 45,319,640

7 unchanged sentences

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

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

5 unchanged sentences

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 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 three and six months ended June 30, 2024.

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

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

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Amortization Period

June 30, 2025:

September 30, 2025:

Developed technology $ 111,102 $ ( 49,580 ) $ 61,522 6.9

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(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):

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):

Remainder of 2025 $ 4,673

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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.

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.

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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 June 30, Six Months Ended June 30,

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

2025 2024 2025 2024

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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 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.

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

Time-based Stock Options

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:

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:

(in Thousands)

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Forfeited ( 72,828 ) 36.96

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

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

(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 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,

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 %

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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

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

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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.

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”).

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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 six months ended June 30, 2025 is presented below:

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

Shares Weighted

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Forfeited ( 1,257,045 ) 57.49

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.

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.

Performance-based Restricted Stock Units

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Notes to Condensed Consolidated Financial Statements

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

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

Shares Weighted

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Forfeited ( 840,064 ) 7.81

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.

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.

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

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

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

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

1 unchanged sentence

Forfeited ( 859 ) 512.62

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.

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.

Ginkgo Bioworks Holdings, Inc.

3 unchanged sentences

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

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

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

2025 2024 2025 2024

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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 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 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’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.

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

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

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

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

customers accounted for 76 % and 84 %, respectively.

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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 June 30, 2025 and December 31, 2024.

The Company had no contract asset balances as of September 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 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.

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.

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.

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.

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.

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 June 30, 2025 and December 31, 2024 was $ 102.1 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 September 30, 2025 and December 31, 2024 was $ 81.3 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 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;

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;

$ 12.8 million between 2025 and 2026;

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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 June 30, Six Months Ended June 30,

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

2025 2024 2025 2024

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

(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.

(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.

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

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

Net Loss per Share

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

Ginkgo Bioworks Holdings, Inc.

Notes to Condensed Consolidated Financial Statements

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

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

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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 June 30,

As of September 30,

Unvested PSUs 4,653,829 —

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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 June 30, 2025 As of December 31, 2024

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

Deferred revenue, current and non-current:

5 unchanged sentences

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 June 30, Six Months Ended June 30,

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

2025 2024 2025 2024

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

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

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.

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.

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.

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