BOSTON, Mass – November 12, 2024 – Ginkgo Bioworks Holdings, Inc. (NYSE: DNA, “Ginkgo”), which is building the leading platform for cell programming and biosecurity, today announced its results for the third quarter ended September 30, 2024. The update, including a webcast slide presentation with additional details on the third quarter and supplemental financial information will be available at investors.ginkgobioworks.com.

•Third quarter 2024 Total revenue of $89 million, up from $55 million in the comparable prior year period, an increase of 61% driven by $45 million of non-cash revenue from a release of deferred revenue relating to the mutual termination of a customer agreement. Excluding this impact, Total revenue in the quarter was $44 million, a decrease of 21% over the prior year period

◦Excluding the $45 million non-cash deferred revenue release, third quarter 2024 Cell Engineering revenue of $30 million, down from $37 million in the comparable prior year period, a decrease of 20% driven by the continued shift from early stage customers to large/enterprise customers along with commercial changes related to the restructuring

◦Third quarter 2024 Biosecurity revenue of $14 million with gross profit margin of 28%. Biosecurity revenue decreased from the comparable prior year period due to the expected ramp down of K-12 testing

•Third quarter 2024 Loss from operations of $(55) million (inclusive of stock-based compensation expense of $14 million and M&A and restructuring related costs of $2 million, net), compared to Loss from operations of $(286) million (inclusive of stock-based compensation expense of $54 million and M&A and restructuring related costs, including asset impairments, of $124 million) in the comparable prior year period. The 2024 period also benefited from the above non-cash deferred revenue release

•Third quarter 2024 Adjusted EBITDA of $(20) million, up from $(84) million in the comparable prior year period, driven by the above non-cash deferred revenue release and a decrease in operating expenses

•Cash and cash equivalents balance as of the end of the third quarter of $616 million

“I’m extremely proud of the significant progress we made in the third quarter,” said Jason Kelly, co-founder and CEO of Ginkgo. “The team has been laser-focused on delivering for customers while driving down costs even further. We are achieving ambitious milestones, signing new deals with several new and existing customers while also launching our new Automation, Datapoints and AI offerings. Beyond customer successes, we will substantially consolidate our overall real estate footprint by exiting several facilities in Cambridge, MA and Europe by year end. We couldn’t have done this without the support of our Board and we’re very grateful to Arie for all of his service and contributions to our journey since going public, and look forward to working closely with Sri as he brings a wealth of knowledge in the automation and life science tools space as we expand increasingly into tools. It’s an incredibly important time to be pursuing the mission of making biology easier to engineer and creating sustainable biosecurity infrastructure for the future. I am excited by the momentum we are gaining to meet that mission as we close out this year on a substantially reduced cost base.”

•Cell Engineering closed deals with new and existing customers

◦Added 25 new programs and other customer contracts to the Cell Engineering platform in Q3 2024, of which 11 were comparable in size and scope to historically reported New Programs and an additional 14 contracts that represent a variety of other deal archetypes, such as Datapoints projects

◦Signed a new deal with Novo Nordisk focused on the discovery and development of proteins while also expanding Ginkgo’s existing collaboration on expression systems for pharmaceutical products ◦Delivered on a major research milestone for Ginkgo’s previously announced deal with Merck.

As part of this milestone completion, Ginkgo will receive a fee of $9 million in cash, expected in Q4 2024, and will move to Stage 2 to work towards making an even more effective production process

◦Signed three new Datapoints deals with a major TechBio company and two of the top 25 pharmaceutical companies

•Ginkgo Biosecurity continues to work towards creating solutions that offer persistent, pervasive monitoring

◦Ginkgo validated its approach to rapidly detect H5N1 and has updated its offerings to include DNA sequencing of raw milk, bioinformatics as a service and comprehensive analyzed data sets

•Ginkgo made significant progress on its plan to reach Adjusted EBITDA breakeven by the end of 2026

◦The reduction in force is estimated to achieve over $85 million in annualized savings by mid-2025

◦Ginkgo has continued implementing significant non-people cost cutting measures, including rationalizing third-party costs and site consolidation

•Dr. Sri Kosuri, CEO of Octant and former associate professor at UCLA in the Chemistry and Biochemistry Department, joined our Board on November 6, 2024. Dr. Arie Belldegrun, a director since September 2021 and member of our compensation committee, resigned from the Board on November 7, 2024

•Ginkgo previously issued 2024 guidance for Total revenue of $170-190 million; Cell Engineering services revenue of $120-140 million; and Biosecurity revenue of at least $50 million. Ginkgo updates its previously issued guidance solely to reflect the impact of the previously mentioned $45 million non-cash deferred revenue release in the third quarter to:

◦Total revenue guidance of $215-235 million in 2024;

◦Cell Engineering services revenue of $165-185 million in 2024; and

◦Biosecurity revenue of at least $50 million in 2024.

Ginkgo will host a videoconference today, Tuesday, November 12, 2024, beginning at 5:30 p.m. ET. The presentation will include an overview of third quarter financial performance, 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/

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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 is the leading horizontal platform for cell programming, providing flexible, end-to-end services that solve challenges for organizations across diverse markets, from food and agriculture to pharmaceuticals to industrial and specialty chemicals. 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, 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 and profitability, our reduction in workforce and anticipated impacts thereof, the timing and structuring of our facilities consolidation and the potential financial impact thereof, potential customer success, including successful application of our offerings by our customers, expectations with regard to revenue, expenses, including our stock-based compensation expenses, our full year 2024 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, (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, (ix) our ability to successfully develop engineered cells, bioprocesses, data packages or other deliverables, (x) the product development or commercialization success of our customers, and (xi) the potential negative impact on our business of our planned reduction in force or the failure to realize the anticipated savings associated therewith. 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 29, 2024 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 and does not intend 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, 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.

(1)Total stock-based compensation expense, inclusive of employer payroll taxes, was allocated as follows (in thousands):

(1)All periods include non-cash revenue when earned, including $45.4 million in the three and nine months ended September 30, 2024, recognized pursuant to the termination of revenue contracts with Motif.

(2)Includes $0.2 million and $1.1 million in employer payroll taxes for the three months ended September 30, 2024 and 2023, respectively, and $2.9 and $4.3 million for the nine months ended September 30, 2024 and 2023, respectively.

(3)For 2024, includes $47.9 million related to goodwill impairment. For the three months ended September 30, 2023, includes a $16.2 million impairment loss on lab equipment and a $96.2 million impairment loss on an operating lease right-of-use asset and related leasehold improvements associated with an exited Zymergen leased facility. For the nine months ended September 30, 2023, includes a $25.2 million impairment loss on lab equipment and a $96.2 million impairment loss on lease assets associated with the exited Zymergen leased facility.

(4)Restructuring charges consist of employee termination costs from the reduction in force commenced in June 2024, as well as the impairment of a right-of-use asset relating to facilities consolidation.

(5)Represents transaction and integration costs directly related to mergers and acquisitions, including: (i) due diligence, legal, consulting and accounting fees associated with acquisitions, (ii) post-acquisition employee retention bonuses and severance payments, (iii) the fair value adjustments to contingent consideration liabilities resulting from acquisitions, (iv) costs associated with the Zymergen Bankruptcy, as well as securities litigation costs, net of insurance recovery. Not included in this adjustment are non-cash charges for acquired in-process research and development expenses, which totaled $19.8 million and $4.0 million in the nine months ended September 30, 2024 and 2023, respectively.

(1)Includes $0.2 million and $1.1 million in employer payroll taxes for the three months ended September 30, 2024 and 2023, respectively, and $2.9 million and $4.3 million in employer payroll taxes for the nine months ended September 30, 2024 and 2023, respectively.

(2)For 2024, includes $47.9 million related to goodwill impairment. For the three months ended September 30, 2023, includes a $16.2 million impairment loss on lab equipment and a $96.2 million impairment loss on an operating lease right-of-use asset and related leasehold improvements associated with an exited Zymergen leased facility. For the nine months ended September 30, 2023, includes a $25.2 million impairment loss on lab equipment and a $96.2 million impairment loss on lease assets associated with the exited Zymergen leased facility.