Ginkgo Bioworks Reports Third Quarter 2025 Financial Results

Ginkgo provides an update on its third quarter financial results

Ginkgo Bioworks Holdings, Inc. (NYSE: DNA, “Ginkgo”) today announced its results for the third quarter ended September 30, 2025. The update, including a webcast slide presentation with additional details on the third quarter, as well as supplemental financial information will be available at investors.ginkgobioworks.com.

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Third Quarter 2025 Financial Results

— Third quarter 2025 Total revenue of $39 million compared to $89 million in the comparable prior year period, a decrease of 56%, which prior year included $45 million of non-cash revenue from a release of deferred revenue relating to the mutual termination of a customer agreement. Excluding this prior year impact, Total revenue in the third quarter of 2025 decreased 11% from the comparable prior year period.

— Third quarter 2025 Cell Engineering revenue of $29 million compared to $75 million in the comparable prior year period, a decrease of 61%, which prior year included the above noted $45 million of non-cash revenue. Excluding this prior year impact, Cell Engineering revenue in the third quarter of 2025 decreased slightly from the comparable prior year period.

— Third quarter 2025Biosecurity revenue of $9 million compared to $14 million in the comparable prior year period

— Third quarter 2025 GAAP net loss of $(81) million, compared to $(56) million in the comparable prior year period, primarily attributable to the above noted non-cash deferred revenue release in the prior year period

— Third quarter 2025 Adjusted EBITDA of $(56) million, down from $(20) million in the comparable prior year period, primarily attributable to the above noted non-cash deferred revenue release in the prior year period

— Cash, cash equivalents and marketable securities balance as of September 30, 2025 of $462 million

“Our recent partnership announcements are powerful examples of how Ginkgo's AI-enabled cloud lab technology can be deployed to accelerate U.S. scientific innovation,” said Jason Kelly, co-founder and CEO of Ginkgo Bioworks. “The recent AI Action Plan from President Trump specifically called for investment in AI-enabled cloud laboratories to keep the American bioeconomy competitive. Ginkgo's tools are designed to generate the massive, high-quality datasets that modern AI methods need, furthering the goal of the U.S. remaining at the forefront of the bioeconomy.”

Recent Business Highlights & Strategic Positioning

— We believe AI models will impact biotechnology in two ways and Ginkgo is well-positioned to provide tools in both

— First, we see reasoning models controlling lab automation. Since science moves forward on the back of lab data and reasoning models are already capable of planning and analyzing experiments, we believe coupling reasoning models to automation will allow science to move as fast as human ideas.

— Second, we see AI models that predict and generate new biological discoveries. Protein models such asAlphaFold prove the potential of large AI models. These models require the type of large training sets of biological data that Ginkgo provides.

— We continue to offer research solutions on top of our in-house robotics, winning us new deals in Agriculture and with the U.S. Government

— We announced the extension of our multi-year strategic partnership withBayer to continue advancing the research and development of biological products for agriculture. The collaboration, which began in 2017, will build on the success of developing an innovative nitrogen fixation platform, and Bayer continues to be a major partner for Ginkgo's expanded agricultural biologicals R&D platform.

— We were recently awarded a project agreement through the Biomedical Advanced Research and Development Authority's (BARDA) BioMaP-Consortium with a total contract value of up to $22.2 million to develop innovations in monoclonal antibody biomanufacturing and to produce an anti-filovirus medical countermeasure

— We are expanding our frontier autonomous lab in Boston as a showcase. Please visit!

— We'll soon have 46 major instruments on 36Reconfigurable Automation Carts (RACs). With these RACS, we can apply AI reasoning models and “lab in the loop” to your scientific challenges. Upon successful proof-of-concept, we can build and install a system so you can run it at your own site.

— We can have your workflows running on the system in a matter of weeks if we have the required equipment. Reach out for a demo!

Full Year 2025 Outlook

— Ginkgo reaffirms Total revenue of $167-$187 million in 2025

— Ginkgo continues to expect Cell Engineering revenue of $117-$137 million in 2025

— Ginkgo continues to expectBiosecurity revenue of at least $40 million in 2025

Conference Call Details Ginkgo will host a video conference today, Thursday, November 6, 2025, beginning at 4:30 p.m. ET. The presentation will include an overview of the third quarter of 2025, recent business updates, a discussion on Ginkgo's outlook, as well as a moderated question and answer session.

To ask a question ahead of the presentation, please submit your questions to@Ginkgo on X (hashtag #GinkgoResults) or by sending an e-mail toinvestors@ginkgobioworks.com.

A webcast link is available on Ginkgo's Investor Relations website and a replay will be made available following the presentation.

Ginkgo Investor Website: https://investors.ginkgobioworks.com/events/

Audio-Only Dial Ins:

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Webinar ID: 953 3421 4604

If you experience technical difficulties with any of these dial-ins or if you need international dial-in numbers, please visit our website at https://investors.ginkgobioworks.com/events/ for updated dial-in information.

About Ginkgo Bioworks Ginkgo Bioworks builds the tools that make biology easier to engineer for everyone. Ginkgo R&D Solutions delivers customizable R&D packages-such as protein engineering, nucleic acid design, and cell-free systems-giving partners a comprehensive way to accelerate innovation across therapeutics, diagnostics, & manufacturing. Ginkgo Automation sells modular, integrated laboratory automation so scientists can spend their days planning and analyzing experiments rather than pipetting in the lab. Ginkgo Datapoints uses Ginkgo's in-house automation to generate the large lab data sets to power your AI models. Ginkgo Biosecurity is building and deploying the next-generation infrastructure and technologies that global leaders need to predict, detect, and respond to a wide variety of biological threats. For more information, visit ginkgobioworks.com and ginkgobiosecurity.com, read our blog, or follow us on social media channels such as X (@Ginkgo and @Ginkgo_Biosec), Instagram (@GinkgoBioworks), Threads (@GinkgoBioworks), or LinkedIn.

Forward-Looking Statements of Ginkgo Bioworks This press release, the presentation, and the conference call and webcast contain certain forward-looking statements within the meaning of the federal securities laws, including statements regarding our plans, including with respect to technology adaptations to meet our customers' needs, strategies, including with respect to our current expectations, operations and anticipated results of operations, both business and financial, including the timing for attaining Adjusted EBITDA breakeven, impacts of our restructuring, potential customer success, including successful application of our offerings by our customers, expected benefits from our strategic partnerships, and expectations with regard to revenue, including our ability to meet all milestones and achieve the maximum revenue available under certain of our customer arrangements, expenses, our full year 2025 outlook, and the market environment, all of which are subject to known and unknown risks, uncertainties and other factors that may cause our actual results, performance or achievements, market trends, or industry results to differ materially from those expressed or implied by such forward-looking statements. These forward-looking statements generally are identified by the words “believe,” “can,” “project,” “potential,” “expect,” “anticipate,” “estimate,” “intend,” “strategy,” “future,” “opportunity,” “plan,” “may,” “should,” “will,” “would,” “will be,” “will continue,” “will likely result,” and similar expressions. Forward-looking statements are predictions, projections and other statements about future events that are based on current expectations and assumptions and, as a result, are subject to risks and uncertainties. Many factors could cause actual future events to differ materially from the forward-looking statements in this document, including but not limited to: (i) our ability to realize near-term and long-term cost savings associated with our site consolidation plans, including the ability to terminate leases or find sub-lease tenants for unused facilities, (ii) volatility in the price of Ginkgo's securities due to a variety of factors, including changes in the competitive and highly regulated industries in which Ginkgo operates and plans to operate, variations in performance across competitors, and changes in laws and regulations affecting Ginkgo's business, (iii) the ability to implement business plans, forecasts, and other expectations, and to identify and realize additional business opportunities, including with respect to our solutions and tools offerings, (iv) the risk of downturns in demand for products using synthetic biology, (v) the uncertainty regarding the demand for passive monitoring programs and biosecurity services, (vi) changes to the biosecurity industry, including due to advancements in technology, emerging competition and evolution in industry demands, standards and regulations, (vii) the outcome of any pending or potential legal proceedings against Ginkgo, (viii) our ability to realize the expected benefits from and the success of our Foundry platform programs and Codebase assets, (ix) our ability to successfully develop engineered cells, bioprocesses, data packages or other deliverables, (x) the product development, production or manufacturing success of our customers, (xi) our exposure to the volatility and liquidity risks inherent in holding equity interests in other operating companies and other non-cash consideration we may receive for our services, (xii) the potential negative impact on our business of our restructuring or the failure to realize the anticipated savings associated therewith and (xiii) the uncertainty regarding government budgetary priorities and funding allocated to government agencies, including potential adverse effects from the U.S. government shutdown. The foregoing list of factors is not exhaustive. You should carefully consider the foregoing factors and the other risks and uncertainties described in the “Risk Factors” section of Ginkgo's annual report on Form 10-K filed with the U.S. Securities and Exchange Commission (the “SEC”) on February 25, 2025 and other documents filed by Ginkgo from time to time with the SEC. These filings identify and address other important risks and uncertainties that could cause actual events and results to differ materially from those contained in the forward-looking statements. Forward-looking statements speak only as of the date they are made. Readers are cautioned not to put undue reliance on forward-looking statements, and Ginkgo assumes no obligation to update or revise these forward-looking statements, whether as a result of new information, future events, or otherwise. Ginkgo does not give any assurance that it will achieve its expectations.

Use of Non-GAAP Financial Measures Certain of the financial measures included in this release, including Adjusted EBITDA and non-GAAP revenue, have not been prepared in accordance with generally accepted accounting principles (“GAAP”), and constitute “non-GAAP financial measures” as defined by the SEC. Ginkgo has included these non-GAAP financial measures because it believes they provide an additional tool for investors to use in evaluating Ginkgo's financial performance and prospects. Due to the nature and/or size of the items being excluded, such items do not reflect future gains, losses, expenses or benefits and are not indicative of our future operating performance. These non-GAAP financial measures are supplemental to, and should not be considered in isolation from, or as an alternative to, financial measures determined in accordance with GAAP. In addition, these non-GAAP financial measures may differ from non-GAAP financial measures with comparable names used by other companies. See the reconciliation below for additional information regarding certain of the non-GAAP financial measures included in this release, including a description of these non-GAAP financial measures and a reconciliation of the historic measures to Ginkgo's most comparable GAAP financial measures.

Ginkgo Bioworks Contacts:

INVESTOR CONTACT: investors@ginkgobioworks.com

MEDIA CONTACT: press@ginkgobioworks.com

Ginkgo Bioworks Holdings, Inc.Condensed Consolidated Balance Sheets(unaudited)(in thousands, except share data) As of September As of December 30, 2025 31, 2024AssetsCurrent assets:Cash and cash equivalents $ 111,065 $ 561,572Marketable securities 350,797 -Accounts receivable, net 21,430 21,857Accounts receivable – related parties 929 586Prepaid expenses and other current assets 21,861 18,729Total current assets 506,082 602,744Property, plant and equipment, net 176,579 203,720Operating lease right-of-use assets 368,213 394,435Investments 30,175 48,704Intangible assets, net 61,522 72,510Other non-current assets 46,594 55,336Total assets $ 1,189,165 $ 1,377,449Liabilities and Stockholders' EquityCurrent liabilities:Accounts payable $ 10,704 $ 14,169Deferred revenue (includes $311 and $795 from related parties) 25,236 27,710Accrued expenses and other current liabilities 79,341 65,387Total current liabilities 115,281 107,266Non-current liabilities:Deferred revenue, net of current portion (includes $64,786 and $72,260 from related 74,072 98,783parties)Operating lease liabilities, non-current 422,870 438,766Other non-current liabilities 17,159 16,576Total liabilities 629,382 661,391Commitments and contingencies (Note 10)Stockholders' equity:Preferred stock, $0.0001 par value; 200,000,000 shares authorized; none issued – -Common stock, $0.0001 par value (Note 8) 6 5Additional paid-in capital 6,627,350 6,555,416Accumulated deficit (6,069,569) (5,837,557)Accumulated other comprehensive income (loss) 1,996 (1,806)Total stockholders' equity 559,783 716,058Total liabilities and stockholders' equity $ 1,189,165 $ 1,377,449Ginkgo Bioworks Holdings, Inc.Condensed Consolidated Statements of Operations and Comprehensive Loss(unaudited)(in thousands, except share data) Three Months Ended Nine Months Ended September 30, September 30, 2025 2024 2025 2024Cell Engineering revenue (1) $ 29,380 $ 75,089 $ 106,744 $ 139,183Biosecurity revenue 9,457 13,957 30,015 44,013Total revenue 38,837 89,046 136,759 183,196Costs and operating expenses:Cost of Biosecurity revenue 8,177 9,987 25,576 30,996Cost of other revenue 4,625 2,016 14,095 3,930Research and development 69,353 77,006 193,646 347,684General and administrative 44,954 52,292 137,276 188,864Goodwill impairment – – – 47,858Restructuring charges 1,745 2,949 10,692 20,015Total operating expenses 128,854 144,250 381,285 639,347Loss from operations (90,017) (55,204) (244,526) (456,151)Other income (expense):Interest income, net 5,742 9,251 17,906 31,275Gain (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 – 5,701Other income (expense), net (163) 1,572 (5,348) 2,821Total other income (expense) 9,263 (1,574) 12,320 16,502Loss before income taxes (80,754) (56,778) (232,206) (439,649)Income tax (benefit) expense 1 (375) (194) (154)Net loss $ (80,755) $ (56,403) $ (232,012) $ (439,495)Net loss per share:Basic $ (1.45) $ (1.08) $ (4.22) $ (8.58)Diluted $ (1.45) $ (1.08) $ (4.22) $ (8.58)Weighted average common shares outstanding:Basic 55,633,718 52,240,559 54,916,539 51,244,332Diluted 55,633,718 52,246,129 54,916,539 51,249,902Comprehensive loss:Net loss $ (80,755) $ (56,403) $ (232,012) $ (439,495)Other comprehensive (loss) income:Foreign currency translation adjustment 27 494 3,462 (2,713)Reclassification of foreign currency translation – 1,492 – 1,492adjustment realized upon sale of foreignsubsidiaryUnrealized gains (loss) on available-for-sale 316 – 340 -securitiesTotal other comprehensive (loss) income 343 1,986 3,802 (1,221)Comprehensive loss $ (80,412) $ (54,417) $ (228,210) $ (440,716)(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.GinkgoBioworks Holdings, Inc.Condensed Consolidated Statements of Cash Flows(unaudited)(in thousands) Nine Months Ended September 30, 2025 2024Cash flows from operating activities:Net loss $ (232,012) $ (439,495)Adjustments to reconcile net loss to net cash used in operating activities:Depreciation and amortization 45,327 47,368Stock-based compensation 60,519 91,783Goodwill impairment – 47,858Restructuring related impairment charges – 4,823Loss on investments 275 16,282Loss on deconsolidation of subsidiary – 7,013Change in fair value of notes receivable 5,685 -Change in fair value of warrant liabilities – (5,701)Change in fair value of contingent consideration (4,232) 3,698Non-cash lease expense 22,449 20,619Non-cash in-process research and development – 19,796Accretion of discount on marketable securities (2,502)Other non-cash activity 1,611 655Changes in operating assets and liabilities:Accounts receivable 345 (6,101)Prepaid expenses and other current assets (70) 3,487Operating lease right-of-use assets 3,814 19,224Other non-current assets (38) (196)Accounts payable, accrued expenses and other current liabilities 16,991 (31,099)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)Other non-current liabilities 4,459 1,998Net cash used in operating activities (123,381) (277,150)Cash flows from investing activities:Purchases of marketable debt securities (401,838) -Maturities of marketable debt securities 73,599 -Purchases of property and equipment (7,660) (48,831)Business acquisition – (5,400)Proceeds from sales of marketable securities – 3,951Proceeds from sale of equipment – 591Other 511 538Net cash used in investing activities (335,388) (49,151)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 – 84Principal payments on finance leases (329) (694)Contingent consideration payment – (922)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)Net decrease in cash, cash equivalents and restricted cash (448,783) (328,045)Cash and cash equivalents, beginning of period 561,572 944,073Restricted cash, beginning of period 44,171 45,511Cash, cash equivalents and restricted cash, beginning of period 605,743 989,584Cash and cash equivalents, end of period 111,065 616,214Restricted cash, end of period 45,895 45,325Cash, cash equivalents and restricted cash, end of period $ 156,960 $ 661,539Ginkgo Bioworks Holdings, Inc.Segment Information(in thousands, unaudited) Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024Cell EngineeringRevenue $ 29,380 $ 75,089 $ 106,744 $ 139,183Costs and operating expenses:Cost of other revenue 2,994 2,016 9,980 3,930Research and development 50,954 55,137 130,689 221,148General and administrative 12,170 23,088 44,338 94,534Cell Engineering operating loss (36,738) (5,152) (78,263) (180,429)BiosecurityRevenue 9,457 13,957 30,015 44,013Costs and operating expenses:Cost of Biosecurity revenue 7,643 9,987 23,449 30,996Research and development – 141 – 720General and administrative 6,692 10,040 21,443 33,169Biosecurity 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 operatingloss to loss before income taxes:Stock-based compensation (1) 18,103 14,013 61,429 94,636Goodwill impairment – – – 47,858Depreciation and amortization 14,168 17,171 45,327 47,368Restructuring charges (2) 1,745 2,948 10,692 20,015Carrying cost of excess space (net of sublease income) (3) 14,328 9,274 38,416 16,657Merger and acquisition related expense (income) (4) 57 (796) (4,478) 6,110Acquired in-process research and development – – – 19,849Other (income) expense, net (5) (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.(2) See Note 3, Restructuring, for composition of costs.(3) The carrying cost of excess space includes base rent, common area maintenance charges, and real estate taxes associated with facilities the Company is not occupying, net of any sublease income from these spaces.(4) Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs.(5) 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.Selected Non-GAAP Financial Measures(in thousands, unaudited) Three Months Ended Nine Months Ended September 30, September 30,(in thousands) 2025 2024 2025 2024Net loss (1) $ (80,755) $ (56,403) $ (232,012) $ (439,495)Interest income, net (5,742) (9,251) (17,906) (31,275)Income tax (benefit) expense 1 (375) (194) (154)Depreciation and amortization 14,168 17,171 45,327 47,368EBITDA (72,328) (48,858) (204,785) (423,556)Stock-based compensation (2) 18,103 14,013 61,429 94,636Goodwill impairment – – – 47,858Restructuring charges (3) 1,745 2,949 10,692 20,015Merger and acquisition related expense (income) (4) 57 (796) (4,478) 6,110Loss (gain) on investments (3,684) 6,912 238 16,282Loss on deconsolidation of subsidiary – 7,013 – 7,013Change in fair value of warrant liabilities – (1,528) – (5,701)Change in fair value of convertible notes 400 281 5,685 1,127Adjusted EBITDA $ (55,707) $ (20,014) $ (131,219) $ (236,216)(1) All periods include non-cash revenue when earned, including $7.5 million recognized in the nine months ended September 30, 2025, pursuant to the release of deferred revenue related to the mutual termination of a customer agreement.(2) 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 for the nine months ended September 30, 2025 and 2024, respectively.(3) Restructuring charges primarily consist of employee termination costs from the reduction in force commenced in June 2024.(4) Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) legal, consulting, and accounting fees associated with acquisitions; (ii) post-acquisition employee retention bonuses; (iii) (gain)/loss from changes in the fair value of contingent consideration liabilities resulting from acquisitions; and (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs. Not included in this adjustment are acquired in-process research and development expenses, which totaled zero for both the three months ended September 30, 2025 and 2024, respectively, and zero and $19.8 million for the nine months ended September 30, 2025 and 2024, respectively.

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