BOSTON, Mass – November 6, 2025 – 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.

•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 2025 Biosecurity 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."

•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 as AlphaFold 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 with Bayer 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 36 Reconfigurable 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!

•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 expect Biosecurity revenue of at least $40 million in 2025

Ginkgo will host a videoconference 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 to investors@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:

+1 646 876 9923 (New York)

+1 301 715 8592 (Washington DC)

+1 305 224 1968 (Miami)

+1 312 626 6799 (Chicago)

+1 346 248 7799 (Houston)

+1 408 638 0968 (San Jose)

+1 564 217 2000 (Seattle)

+1 689 278 1000 (Orlando)

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.

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.

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.

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

Condensed Consolidated Balance Sheets

(unaudited)

Condensed Consolidated Statements of Operations and Comprehensive Loss

(unaudited)

(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.

Condensed Consolidated Statements of Cash Flows

(unaudited)

(in thousands)

(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.

(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.