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Property of Ginkgo Bioworks — 1Q2 2025 UPDATE & BUSINESS REVIEW Grow with Ginkgo Q3 2025 Update & Business Review November 6, 2025
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Property of Ginkgo Bioworks — 2Q3 2025 UPDATE & BUSINESS REVIEW FORWARD-LOOKING STATEMENTS This presentation, 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. Y ou 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. INDUSTRY AND MARKET DATA In this presentation, Ginkgo relies on and refers to certain information and statistics regarding the markets and industries in which Ginkgo competes. Such information and statistics are based on Ginkgo management’s estimates and/or obtained from third-party sources, including reports by market research firms and company filings. While Ginkgo believes such third-party information is reliable, there can be no assurance as to the accuracy or completeness of the indicated information, and Ginkgo has not independently verified the accuracy or completeness of the information provided by the third-party sources. USE OF NON-GAAP FINANCIAL MEASURES Certain of the financial measures included in this presentation, including Adjusted EBITDA and non-GAAP revenue, cash flow and cash burn 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 included in this presentation for additional information regarding certain of the non-GAAP financial measures included in this presentation, including a description of these non-GAAP financial measures and a reconciliation of the historic measures to Ginkgo’s most comparable GAAP financial measures. TRADEMARKS This presentation may contain trademarks, service marks, trade names and copyrights of other companies, which are the property of their respective owners, and Ginkgo’s use thereof does not imply an affiliation with, or endorsement by, the owners of such trademarks, service marks, trade names and copyrights. Solely for convenience, some of the trademarks, service marks, trade names and copyrights referred to in this presentation may be listed without the TM, © or ® symbols, but Ginkgo will assert, to the fullest extent under applicable law, the rights of the applicable owners, if any, to these trademarks, service marks, trade names and copyrights. Disclaimer
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Property of Ginkgo Bioworks — 3Q3 2025 UPDATE & BUSINESS REVIEW Introduction Jason Kelly, Co-Founder and CEO Q3 2025 Financial Update Steve Coen, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Daniel Marshall, Sr. Manager of Communications and Ownership Agenda
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Property of Ginkgo Bioworks — 4Q3 2025 UPDATE & BUSINESS REVIEW OUR MISSION Make biology easier to engineer OBJECTIVES Deliver the robotics and software that bring autonomous labs on-prem at our bioscience customers though our tools business. Expand our frontier autonomous lab in Boston to demonstrate the latest of what can be done with automation and AI in bioscience. Offer our Solutions and Datapoints customers best-in-class CRO services leveraging our in-house frontier lab.
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Property of Ginkgo Bioworks — 5Q3 2025 UPDATE & BUSINESS REVIEW (73)% QUARTERL Y CASH BURN(1) ($M) Quarterly cash burn continues to improve (Unaudited) Ginkgo remains in a strong financial position with $462 million in cash, cash equivalents, and marketable securities with no bank debt as of Q3 2025 $462M (1) References to cash flow or cash burn for each quarter is defined as change in GAAP cash, cash equivalents, and marketable securities and Company imposed cash restrictions, as adjusted for unrealized equity securities, over such quarter compared to the prior quarter. Cash burn excludes $10M of net proceeds from ATM sales in Q3 2025.
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Property of Ginkgo Bioworks — 6Q3 2025 UPDATE & BUSINESS REVIEW Agenda Introduction Jason Kelly, Co-Founder and CEO Q3 2025 Financial Update Steve Coen, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Daniel Marshall, Sr. Manager of Communications and Ownership
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Property of Ginkgo Bioworks — 7Q3 2025 UPDATE & BUSINESS REVIEW Cell Engineering Highlights (Unaudited) CELL ENGINEERING REVENUE ($M) (61%) REVENUE-GENERATING PROGRAMS (1) (5%) 1) See Appendix for description of revenue-generating programs Includes recognition of $45M non-cash deferred revenue from Motif
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Property of Ginkgo Bioworks — 8Q3 2025 UPDATE & BUSINESS REVIEW BIOSECURITY REVENUE ($M) BIOSECURITY SEGMENT GROSS MARGIN(1) *Map is not exhaustive; some partnerships remain confidential. Data updated 11/01/25 10 Key international airports 46 Collection nodes (cumulative 2025) 15.4M+ Samples to date 100K+ Samples sequenced to date KEY METRICS 27K+ Pathogen Genomes sequenced to date Biosecurity Highlights (Unaudited) Ginkgo HQ Boston 129 Countries of origin of flights sampled (65% OF NATIONS GLOBALLY) 1) Calculated as (Biosecurity Segment Revenue - Segment Cost of Biosecurity Revenue) / (Biosecurity Segment Revenue)
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Property of Ginkgo Bioworks — 9Q3 2025 UPDATE & BUSINESS REVIEW Q3 2025 Financial Summary (Unaudited) 1) Nine months ended September 30, 2025 includes $7.5 million of non-cash revenue from a release of deferred revenue relating to the mutual termination of a customer agreement with BiomEdit. Three months and nine months ended September 30, 2024 include $45M of non-cash revenue from a release of deferred revenue related to the mutual termination of a customer agreement with Motif. 2) For a reconciliation of segment operating expenses, segment operating loss, net loss and Adjusted EBITDA, see the Appendix. Three Months Ended September 30, Nine Months Ended September 30, In millions of USD 2025 2024 % Y oY 2025 2024 % Y oY Revenue: Cell Engineering ⁽¹⁾ $29 $75 (61%) $107 $139 (23%) Biosecurity 9 14 (32%) 30 44 (32%) Total revenue 39 89 (56%) 137 183 (25%) Cell Engineering cost of other revenue 3 2 49% 10 4 154% Cell Engineering research and development 51 55 (8%) 131 221 (41%) Cell Engineering general and administrative 12 23 (47%) 44 95 (53%) Biosecurity cost of sales 8 10 (23%) 23 31 (24%) Biosecurity operating expenses 7 10 (34%) 21 34 (37%) Total segment operating expenses ⁽²⁾ 80 100 (20%) 230 384 (40%) Cell Engineering operating loss (Adjusted EBITDA) (37) (5) (613%) (78) (180) 57% Biosecurity operating loss (Adjusted EBITDA) (5) (6) 21% (15) (21) 29% Total segment operating loss (Adjusted EBITDA) ⁽²⁾ (42) (11) (266%) (93) (201) 54% Net loss (GAAP) ⁽²⁾ (81) (56) (43%) (232) (439) 47% Total Adjusted EBITDA ⁽¹⁾⁽²⁾ (56) (20) (178%) (131) (236) 44% Memo: inclusive of carrying cost of excess space (net of sublease income) 14 9 38 17 Memo: inclusive of M&A related non-cash IP R&D (0) 0 (0) 20 Capital expenditures (net of tenant improvement allowance) 0 10 (100%) 4 30 (87%)
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Property of Ginkgo Bioworks — 10Q3 2025 UPDATE & BUSINESS REVIEW Adjusted EBITDA (Unaudited) TOTAL ADJUSTED EBITDA(1) ($M) (1) For a reconciliation of Adjusted EBITDA, see the Appendix (2) Excludes non-cash IPR&D charge for comparison purposes to other periods shown (3) References to cash flow or cash burn for each quarter is defined as change in GAAP cash, cash equivalents, and marketable securities and Company imposed cash restrictions, as adjusted for unrealized equity securities, over such quarter compared to the prior quarter (4) Inclusive of $10M of net proceeds from ATM sales Q1 2024 Q4 2024 Q1 2025 Q2 2025 Q3 2025 Cell Engineering segment ($92) ($38) ($32) ($10) ($37) Biosecurity segment ($11) ($10) ($5) ($5) ($5) Unallocated: excess space + other $3(2) ($9) ($11) ($13) ($14) Total Adj. EBITDA ($100)(2) ($57) ($47) ($28) ($56) TOTAL ADJUSTED EBITDA(1) BY COMPONENT ($M) 2% (32)% Total Adj. EBITDA(1) ($100M)(2) ($57M) ($47M) ($28M) ($56M) Total Cash Flow(3) ($104M) ($55M) ($58M) ($44M) ($18M)(4) Total Revenue Expenses (incl. Cost of Sales)
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Property of Ginkgo Bioworks — 11Q3 2025 UPDATE & BUSINESS REVIEW Historical Outlook In millions of USD FY2024 FY2025 Revenue Cell Engineering $174 $117-137 Services $129 $110-130 Platform venture non-cash deferred revenue release $45 $7 Biosecurity $53 $40+ Total revenue $227 $167-187 Ginkgo reaffirms total revenue guidance
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Property of Ginkgo Bioworks — 12Q3 2025 UPDATE & BUSINESS REVIEW Agenda Introduction Jason Kelly, Co-Founder and CEO Q3 2025 Financial Update Steve Coen, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Daniel Marshall, Sr. Manager of Communications and Ownership
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Property of Ginkgo Bioworks — 13Q3 2025 UPDATE & BUSINESS REVIEW 1 2 3 We continue to offer research solutions on top of our in-house robotics, winning us new deals in Agriculture and with the US Government. We believe AI models will impact biotechnology in two ways and Ginkgo is well-positioned to provide tools in both. We are expanding our frontier autonomous lab in Boston as a showcase. Please visit! 13
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Property of Ginkgo Bioworks — 14Q3 2025 UPDATE & BUSINESS REVIEW 1 2 3 We continue to offer research solutions on top of our in-house robotics, winning us new deals in Agriculture and with the US Government. We believe AI models will impact biotechnology in two ways and Ginkgo is well-positioned to provide tools in both. We are expanding our frontier autonomous lab in Boston as a showcase. Please visit! 14
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Property of Ginkgo Bioworks — 15Q3 2025 UPDATE & BUSINESS REVIEW Research Solutions Datapoints ReagentsAutomation Asset Licensing HIGHER LOWER Service Fees Only Service Fees + Royalties + MilestonesSOLUTIONS TOOLS PRODUCT OFFERING GINKGO CUSTOMIZATION & TECH RISK Enables partners to optimize candidates to take forward into development and enable better manufacturing platforms. [Research Partnership] Enable customers’ scientists to pursue high-throughput data generation. [CRO model] Proprietary lab automation workflows in customer facilities. [Equipment Vendor] Cell free protein synthesis kit, cell lines, RNAP, and more. [Reagents] Cell Engineering Solutions Cell Engineering Tools In 2024, Ginkgo expanded our business model into the life science tools and services space - our tools in your hands!
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Property of Ginkgo Bioworks — 16Q3 2025 UPDATE & BUSINESS REVIEW If AI opens the door to increasing the rate of scientific progress, it’s the most important work we can do Invest in AI-Enabled Science “Like many other domains, science itself will be transformed by AI…. Basic science today is often a labor-intensive process; the AI era will require more scientific and engineering research to transform theories into industrial-scale enterprises. This, in turn, will necessitate new infrastructure and support of new kinds of scientific organizations. Recommended Policy Actions ● Through NSF, DOE, NIST at DOC, and other Federal partners, invest in automated cloud-enabled labs for a range of scientific fields, including engineering, materials science, chemistry, biology, and neuroscience, built by, as appropriate, the private sector, Federal agencies, and research institutions in coordination and collaboration with DOE National Laboratories.”
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Property of Ginkgo Bioworks — 17Q3 2025 UPDATE & BUSINESS REVIEW Biotech will be the 1st battleground for AI-enabled science (robots>>hands)
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Property of Ginkgo Bioworks — 18Q3 2025 UPDATE & BUSINESS REVIEW Two broad categories where AI models will impact biotechnology Reasoning models controlling lab automation ● Science moves forward on the back of lab data. ● Reasoning models are already capable of planning and analyzing experiments. ● Coupling reasoning models to automation allows science to move as fast as human ideas. 1 [Human query] → LLM reasoning → Agentic AI → Real world lab automation → Data generation (loop)
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Property of Ginkgo Bioworks — 19Q3 2025 UPDATE & BUSINESS REVIEW Optional HEPA Filter Utility routing (electrical, air, and data) Plate transport track Quick connection points enable system reassembly in minutes, not days Dedicated robotic arm improves reliability and throughput Lab device of choice, from any application or vendor Local compute to aid reconfigurability RACs solve the challenges of static workcell systems with their reliable, customizable, modular architecture enabling scale and flexibility
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Property of Ginkgo Bioworks — 20Q3 2025 UPDATE & BUSINESS REVIEW Linear RAC System (2-5 RACs) Closed Loop RAC System (10-20 RACs) Mega RAC “One-of-Everything” System (100+ RACs) AI-controlled (“lab in the loop”) labs can start small and grow big. Models can access all bench devices available to scientists. Note: Mega RAC system is currently being designed for a real customer site
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Property of Ginkgo Bioworks — 21Q3 2025 UPDATE & BUSINESS REVIEW AI models that predict and generate new biological discoveries ● Protein models such as AlphaFold prove the potential of large AI models ● Require sufficiently large training sets of biological data ● How far can we push it? Two broad categories where AI models will impact biotechnology 2 Large bio datasets → Modeling → New scientific insights Ginkgo ICML Workshop paper: Good predictive models create good guided generative models Hosted with 🤗 Hugging Face
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Property of Ginkgo Bioworks — 22Q3 2025 UPDATE & BUSINESS REVIEW [ GINKGO DATAPOINTS ] datapoints.ginkgo.bio DOWNLOAD OUR DATASETS Join the community ! Download data for free, read publications, try out models. Let’s build great things together.
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Property of Ginkgo Bioworks — 23Q3 2025 UPDATE & BUSINESS REVIEW 1 2 3 We continue to offer research solutions on top of our in-house robotics, winning us new deals in Agriculture and with the US Government. We believe AI models will impact biotechnology in two ways and Ginkgo is well-positioned to provide tools in both. We are expanding our frontier autonomous lab in Boston as a showcase. Please visit! 23
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Property of Ginkgo Bioworks — 24Q3 2025 UPDATE & BUSINESS REVIEW Research Solutions Datapoints ReagentsAutomation Asset Licensing HIGHER LOWER Service Fees Only Service Fees + Royalties + MilestonesSOLUTIONS TOOLS PRODUCT OFFERING GINKGO CUSTOMIZATION & TECH RISK Enables partners to optimize candidates to take forward into development and enable better manufacturing platforms. [Research Partnership] Enable customers’ scientists to pursue high-throughput data generation. [CRO model] Proprietary lab automation workflows in customer facilities. [Equipment Vendor] Cell free protein synthesis kit, cell lines, RNAP, and more. [Reagents] Cell Engineering Solutions Cell Engineering Tools In 2024, Ginkgo expanded our business model into the life science tools and services space - our tools in your hands!
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Property of Ginkgo Bioworks — 25Q3 2025 UPDATE & BUSINESS REVIEW BARDA Awards Ginkgo and its Partners $22.1M to Onshore Advanced Manufacturing of Key Medical Countermeasures Ginkgo’s AI-enabled cloud lab to enhance domestic production of medicines (mAbs) developed to protect against filoviruses such as Ebola
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Property of Ginkgo Bioworks — 26Q3 2025 UPDATE & BUSINESS REVIEW DISCOVERY AGAINST A TARGET MODE OF ACTION CHARACTERI- ZATION IN VITRO / IN PLANTA TESTING POTENCY, COGS, STABILITY OPTIMIZATION REGULATORY APPROVAL OUR R&D PLATFORM FOR AGRICULTURE COMMERCIAL MANUFACTURING* *up to 3,000L
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Property of Ginkgo Bioworks — 27Q3 2025 UPDATE & BUSINESS REVIEW Source: agfundernews.com Michael Miille, GM of Ginkgo’s Agriculture Business Unit, interviewed in AgFunderNews
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Property of Ginkgo Bioworks — 28Q2 2025 UPDATE & BUSINESS REVIEW Ginkgo Solutions scientists can help apply our lab automation to your hardest R&D challenges in Agriculture, Industrial Biotechnology, and Biopharma.
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Property of Ginkgo Bioworks — 29Q3 2025 UPDATE & BUSINESS REVIEW 1 2 3 We continue to offer research solutions on top of our in-house robotics, winning us new deals in Agriculture and with the US Government. We believe AI models will impact biotechnology in two ways and Ginkgo is well-positioned to provide tools in both. We are expanding our frontier autonomous lab in Boston as a showcase. Please visit! 29
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Property of Ginkgo Bioworks — 30Q3 2025 UPDATE & BUSINESS REVIEW We have been expanding our frontier autonomous lab
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Property of Ginkgo Bioworks — 31Q3 2025 UPDATE & BUSINESS REVIEW [ GINKGO AUTOMATION ] We'll soon have 46 major instruments on 36 RACs.
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Property of Ginkgo Bioworks — 32Q3 2025 UPDATE & BUSINESS REVIEW [ GINKGO AUTOMATION ] The Total System in Action
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Property of Ginkgo Bioworks — 33Q3 2025 UPDATE & BUSINESS REVIEW [ GINKGO AUTOMATION ] If we have the required equipment, we can have your workflows running on the system in a matter of weeks.
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Property of Ginkgo Bioworks — 34Q3 2025 UPDATE & BUSINESS REVIEW Automation The foundation of your data factory: flexible and extensible automation that works We can apply AI Reasoning Models + “Lab in the Loop” to your scientific challenges. Try before you buy – reach out for a demo! LLM + Reasoning Radically change the way scientists get experiments done: fewer meetings and more data Closed-Loop Science Give your tech stack an objective and walk away: instantly kick off the next round of experiments Closed-Loop Science Automated Execution Programmatic Data Egress AI Decision Making Parameterized Protocols [ GINKGO AUTOMATION ]
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Property of Ginkgo Bioworks — 35Q3 2025 UPDATE & BUSINESS REVIEW Agenda Introduction Jason Kelly, Co-Founder and CEO Q3 2025 Financial Update Steve Coen, CFO Strategic Review Jason Kelly, Co-Founder and CEO Q&A Session Moderated by Daniel Marshall, Sr. Manager of Communications and Ownership
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Property of Ginkgo Bioworks — 36Q2 2025 UPDATE & BUSINESS REVIEW APPENDIX
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Property of Ginkgo Bioworks — 37Q3 2025 UPDATE & BUSINESS REVIEW In millions of USD, except % of total Three Months Ended September 30, Nine Months Ended September 30, 2025 % of Total 2024 % of Total 2025 % of Total 2024 % of Total Related Parties $ 0 0% $ 47 62% $ 9 8% $ 52 37% Third Parties 29 100% 28 38% 98 92% 87 63% Cell Engineering Revenue $ 29 100% $ 75 100% $ 107 100% $ 139 100% Cash consideration $ 29 100% $ 27 36% $ 97 91% $ 79 57% Non-cash consideration 0 0% 48 64% 10 9% 60 43% Cell Engineering Revenue $ 29 100% $ 75 100% $ 107 100% $139 100% Related Parties: Related parties include Platform Ventures and certain Structured Partnerships. See notes to our consolidated financial statements in our Quarterly Report on Form 10-Q for the quarter ended September 30, 2025 for additional information related to transactions with related parties. Third Parties: Includes all other customers. Non-Cash Consideration: Cell Engineering revenue recognized relating to contracts in which the underlying consideration is non-cash based, inclusive of downstream value share milestone payments received in the form of equity securities. See notes to our consolidated financial statements in our Quarterly Report on Form 10-Q for the quarter ended September 30, 2025 for additional information related to revenue recognition. Cell Engineering Revenue (Unaudited)
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Property of Ginkgo Bioworks — 38Q3 2025 UPDATE & BUSINESS REVIEW Cell Engineering Revenue-Generating Program Count(1) (1) Chart depicts our historically reported Current Active Programs, expanded to include programs previously referred to as “Other Contracts”, and further adjusted to exclude programs which were not revenue-generating in the quarter. The data presented on this slide are subject to change if this metric is adjusted, management learns new information, or otherwise.
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Property of Ginkgo Bioworks — 39Q3 2025 UPDATE & BUSINESS REVIEW Segment Information (Unaudited) Note: The accompanying footnotes are provided on the next slide Three Months Ended September 30, Nine Months Ended September 30, In millions of USD 2025 2024 2025 2024 Cell Engineering Revenue $29 $75 $107 $139 Costs and operating expenses: Cost of other revenue 3 2 10 4 Research and development 51 55 131 221 General and administrative 12 23 44 95 Cell Engineering operating loss (37) (5) (78) (180) Biosecurity Revenue 9 14 30 44 Costs and operating expense: Cost of Biosecurity revenue 8 10 23 31 General and administrative 7 10 21 34 Biosecurity operating loss (5) (6) (15) (21) Total segment operating loss (42) (11) (93) (201) Reconciling items to reconcile total segment operating loss to loss before income taxes: Depreciation and amortization 14 17 45 47 Stock-based compensation (1) 18 14 61 95 Impairment expense (2) 0 0 0 48 Restructuring charges (3) 2 3 11 20 Carrying cost of excess space (net of sublease income) (4) 14 9 38 17 Merger and acquisition related expenses (income) (5) 0 (1) (4) 6 Acquired in-process research and development 0 0 0 20 Other (income) expense, net (6) (9) 3 (12) (14) Loss before income taxes (81) (57) (232) (440)
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Property of Ginkgo Bioworks — 40Q3 2025 UPDATE & BUSINESS REVIEW 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 the nine months ended September 30, 2025 and 2024, respectively. 2) Includes $47.9 million related to goodwill impairment in the nine months ended September 30, 2024. 3) Restructuring charges primarily consist of employee termination costs from the reduction-in-force commenced in June 2024. 4) 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. 5) 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. 6) Includes interest income, interest expense, loss on investments, changes in fair value of certain assets and liabilities, and other gains and losses. Segment Information Footnotes
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Property of Ginkgo Bioworks — 41Q3 2025 UPDATE & BUSINESS REVIEW 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 and $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 $0.3 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 the nine months ended September 30, 2025 and 2024, respectively. 3) Impairment expense includes $47.9 million related to goodwill impairment in the nine months ended September 30, 2024. 4) Restructuring charges primarily consist of employee termination costs from the reduction-in-force commenced in June 2024. 5) 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, * As adjusted to reflect the impact of including in Adjusted EBITDA the non-cash one-time charges related to acquired in-process research and development (see Footnote 5 below). Adjusted EBITDA Reconciliation (Unaudited) Three Months Ended September 30, Nine Months Ended September 30, In millions of USD 2025 2024 2025 2024 Net loss ⁽¹⁾ $ (80.8) $ (56.4) $ (232.0) $ (439.5) Interest income, net 5.7 9.3 (17.9) (31.3) Income tax expense 0.0 (0.4) (0.2) (0.2) Depreciation and amortization 14.2 17.2 45.3 47.4 EBITDA $ (72.3) $ (48.9) $ (204.8) $ (423.6) Stock-based compensation ⁽²⁾ 18.1 14.0 61.4 94.6 Impairment expense ⁽³⁾ 0.0 0.0 0.0 47.9 Restructuring charges (4) 1.7 2.9 10.7 20.0 Merger and acquisition related expenses (5) 0.1 (0.8) (4.5) 6.1 Loss on investments (3.7) 6.9 0.2 16.3 Loss (gain) on deconsolidation of subsidiaries 0.0 7.0 0.0 7.0 Change in fair value of warrant liabilities 0.0 (1.5) 0.0 (5.7) Change in fair value of convertible notes 0.4 0.3 5.7 1.1 Adjusted EBITDA $ (55.7) $ (20.0) $ (131.2) $ (236.2)