Executive Summary

Q2 revenue beat and margin inflection: Revenue $15.33M, above S&P Global consensus $14.18M, on strong Pharma Biocatalysis demand and a licensing agreement; product gross margin expanded to 72% from 45% YoY, driving a materially lower net loss ($13.3M vs $22.8M YoY) . Consensus figures from S&P Global.*
EPS modestly missed: GAAP EPS of -$0.16 versus -$0.15 consensus as operating investments continued; management reiterated FY25 revenue guidance of $64–$68M and flagged continued quarterly lumpiness as ECO ramps . Consensus figures from S&P Global.*
Strategic momentum in ECO Synthesis and ligase: “Well over 30” ECO engagements (deck indicated 34), expanding ligase wins, and multiple CDMOs demonstrating transferability; management evaluating capacity expansion (ECO Lab #2, potential Codexis-owned GMP) to capture demand .
Balance sheet strengthened: $66.3M cash and investments at 6/30; company raised $27.3M via ATM and Innovatus loan to support ECO expansion and a path to GMP-grade siRNA .

What Went Well and What Went Wrong

What Went Well
- Revenue and margin outperformance: Q2 revenue $15.33M vs $7.98M YoY; product gross margin 72% vs 45% YoY as mix shifted toward more profitable products and away from legacy lines .
- Commercial validation and pipeline build: “Well over 30” ECO engagements and several new ligase customers expected before YE; three CDMO collaborators highlighted ECO/ligase at TIDES, underscoring transferability and performance .
- Stronger liquidity and reiterated outlook: $66.3M cash/investments; FY25 revenue guide reiterated at $64–$68M; management emphasized path to cash flow breakeven by end-2026, with discussion of potentially prioritizing value creation over near-term breakeven as ECO scales .
- Management quote: “Our second quarter results are strong… revenue is above consensus and our operating loss is halved compared to Q2 2024… the objective of cash flow breakeven by 2026 is attainable” .
What Went Wrong
- EPS slight miss and continued operating losses: EPS of -$0.16 missed by $0.01; net loss $13.3M as R&D expense rose with higher headcount and reclassification . Consensus figures from S&P Global.*
- Visibility/lumpiness persists: Management reiterated that quarter-to-quarter revenue will remain variable due to large order timing in the heritage business (biocatalysis), though expected to mitigate as ECO revenue scales .
- Capacity constraints near-term: Demand for ECO may exceed current capacity; company is exploring options (ECO Lab #2, Codexis-owned GMP path) to avoid bottlenecks and retain value in supplying siRNA directly .

Financial Results

Headline P&L and Margins (chronological: oldest → newest)

Metric	Q2 2024	Q1 2025	Q2 2025
Total Revenues ($M)	$7.98	$7.54	$15.33
Net Loss per Share ($)	$(0.32)	$(0.25)	$(0.16)
Product Gross Margin %	45%	55%	72%
R&D Expense ($M)	$11.4	$12.9	$13.8
SG&A Expense ($M)	$15.7	$12.4	$12.3
Net Loss ($M)	$(22.76)	$(20.69)	$(13.27)

Revenue Mix

Revenue ($M)	Q2 2024	Q1 2025	Q2 2025
Product Revenue	$6.26	$6.06	$7.38
R&D Revenue	$1.72	$1.48	$7.95
Total Revenues	$7.98	$7.54	$15.33

Notes: Q2 uplift included higher legacy agreement revenue and a new licensing agreement, alongside variability in customer manufacturing schedules and trial progression .

Liquidity

Liquidity ($M)	Q1 2025 (Mar 31)	Q2 2025 (Jun 30)
Cash, Cash Equivalents & Short-term Investments	$59.8	$66.3

Raised $27.3M via ATM and Innovatus loan to support ECO expansion and path to GMP-grade supply .

Guidance Changes

Metric	Period	Previous Guidance	Current Guidance	Change
Total Revenues	FY 2025	$64–$68M (2/27)	Reiterated $64–$68M (8/13)	Maintained
Product Gross Margin	FY 2025 vs 2024	Improve vs 2024 (2/27)	Expect FY25 gross margins to improve vs 2024 (8/13)	Maintained
Cash Runway / Cash Flow	Multi-year	Sufficient through positive cash flow by end-2026 (5/14)	Sufficient to fund planned operations through 2027 (8/13)	Raised runway
Milestone: GLP pilot	2025	Pilot-scale GLP-grade siRNA in 2025	Reiterated 2025 pilot-scale GLP-grade material (Q2 PR)	Maintained
Milestone: GMP scale-up partner	2025 YE	Sign GMP scale-up partner by YE 2025	Reiterated target to sign by YE 2025 (Q2 PR)	Maintained

Earnings Call Themes & Trends

Topic	Previous Mentions (Q-2 and Q-1)	Current Period (Q2 2025)	Trend
ECO Synthesis commercialization	Q4: ECO Innovation Lab commissioned; plan to convert collabs to contracts, target GLP pilot in 2025, GMP partner by YE25 . Q1: Signed first ECO revenue contract; adoption path emphasized via CDMOs; reproducibility/quality data to be showcased at TIDES .	Well over 30 ECO engagements; “ECO business is lifting off”; exploring capacity expansion (ECO Lab #2, potential Codexis-owned GMP) to meet demand .	Improving
Ligase traction	Q1: First large pharma ligase order and second innovator order; ML tool launched to optimize ligase/fragment design .	Several new ligase customers expected by YE; multiple CDMOs validated transferability/performance in-house .	Improving
CDMO partnerships	Q4/Q1: CDMOs a key wedge; co-presentations planned; transferability emphasized .	Three CDMOs highlighted ECO/ligase; more CDMOs in discussions beyond initial three .	Improving
Margins and mix	Q4: Product GM 63% on mix; 2025 to demonstrate growth via ligase/GLP . Q1: GM 55%; mix shifting to profitable products .	GM 72% in Q2; expect FY25 GM to improve vs 2024; caution on sustainability of Q2 step-up .	Improving, with caution
Cash runway & financing	Q4/Q1: Cash expected to fund to positive cash flow by end-2026 .	Raised $27.3M (ATM + Innovatus); runway extended to fund operations through 2027 .	Strengthened
Supply chain/onshoring	Q1: ECO supports onshoring with reduced capex, less China dependence; pursuing enzymatic inputs supply .	Continued emphasis on onshoring and scalable path to GMP-grade material .	Stable/positive
AI/ML enablement	Q1: ML tool for ligase selection/fragment design; broader data science to accelerate process .	ML-driven ligase selection cited as customer win driver; broader AI viewed as moat with know-how .	Improving

Management Commentary

CEO (Stephen Dilly): “Our second quarter results are strong… revenue is above consensus and our operating loss is halved compared to Q2 2024… demand for ECO will rapidly exceed our ability to supply… we’re exploring options that would expand our bandwidth… The clearest path… is to lock in as many early phase product[s] as we can onto the ECO platform” .
COO (Kevin Norrett): “Strong Q2 revenue… driven by increasing orders for enzymes supporting late phase and commercialized APIs… We expect to add several new ligase customers before the end of the year… our Ecosynthesis business is lifting off” .
CFO (Georgia Erbez): “Total revenue… was $15.3M vs. $8.0M [YoY]… Product gross margin was 72%… we do not anticipate this magnitude of change to be sustained over the entire year… reiterating our 2025 guidance… we ended the quarter with $66.3M in cash, cash equivalents and investments… sufficient to fund… through 2027” .

Q&A Highlights

Pipeline/engagements: “Well over 30” ECO discussions, “growing into the 40s”; mix includes CDMOs, large drug innovators, stealth/small biotechs; ability to be selective given breadth .
Capacity path: Considering ECO Lab #2; Codexis-owned GMP could enable seamless scale-up and serve small/medium innovators through Ph1/2; building “just-in-time” capacity to match pipeline maturation .
Revenue phasing/guide cadence: Growth expected in 2H from ligase and ECO; Q/Q lumpiness remains; “average guidance on the Street… within the range of reasonableness” .
Monetization model: Early phase focus de-emphasizes near-term revenue to maximize long-term value via direct siRNA supply; milestones and material supply in early phases; transitions to volume-based pricing as programs progress .
Financing and optionality: $27.3M “modest, targeted” top-up to secure infrastructure and capability build-out; biocatalysis remains profitable engine reducing cash needs; CDMO/ligase contracts help fund scaling .

Estimates Context

Q2 2025 vs S&P Global consensus: Revenue $15.33M vs $14.18M consensus; EPS $(0.16) vs $(0.15) consensus; FY25 revenue consensus ~$66.3M.* Actual revenue was highlighted as above consensus in the company’s materials . Consensus figures from S&P Global.*

Metric	Q2 2025 Consensus*	Q2 2025 Actual	Surprise*
Revenue ($M)	$14.18*	$15.33	+$1.15M (+8.1%)*
EPS ($)	$(0.15)*	$(0.16)	Miss by $0.01*

Metric	Q1 2025 Consensus*	Q1 2025 Actual	Surprise*
Revenue ($M)	$9.66*	$7.54	-$2.12M (-22%)*
EPS ($)	$(0.208)*	$(0.25)	Miss by $0.04*

Metric	Q2 2024 Consensus*	Q2 2024 Actual	Surprise*
Revenue ($M)	$7.82*	$7.98	+$0.16M (+2%)*
EPS ($)	$(0.238)*	$(0.32)	Miss by $0.08*

Values with asterisks were retrieved from S&P Global. Surprises are computed versus S&P Global consensus.*

Key Takeaways for Investors

Q2 execution reset the trajectory: major revenue beat and sharp margin expansion while maintaining expense discipline, supporting the FY25 guide and improving loss profile .
The narrative is shifting from technical validation to commercialization: CDMO proof points and rising ECO/ligase demand suggest 2H revenue contribution from ECO themes, albeit with quarterly variability .
Strategic choice ahead: management is weighing near-term cash breakeven vs. maximizing long-term value by scaling ECO capacity and remaining a direct siRNA supplier; any announced capacity build (ECO Lab #2/GMP) likely a stock catalyst .
Estimate revisions: Street likely to lift revenue forecasts modestly on Q2 beat and back-half commentary, while EPS remains pressured near term as R&D scales to meet ECO demand.*
De-risking factors: cash runway extended through 2027 and additional $27.3M raised reduce financing overhang; profitable biocatalysis engine continues to fund ECO build-out .
Watch list into 2H: pace of new ligase wins, signing of additional ECO Innovation Lab customers, announcement of GMP scale-up partner, and any update on Codexis-owned GMP plans .
Medium-term thesis: If Codexis locks in early-phase programs and remains the direct siRNA source through clinical maturation, the revenue slope and margin profile could structurally improve with scale .

Appendix: Other Relevant Q2 2025 Items

Investor events: Participation at Cantor Global Healthcare Conference (Sep 3–5, 2025), with webcast and replay .
Press release details: Q2 PR reiterated milestones (GLP pilot 2025, GMP partner by YE25) and highlighted $27.3M capital raise to support ECO expansion .

Notes on sources: Financials, guidance, and management commentary are sourced from the company’s Q2 earnings press release, 8-K filing, and earnings call transcript –. Prior quarter/year comparatives and guidance history are from Q1 and Q4 materials – –. Consensus estimates and surprises are from S&P Global.*

CODEXIS, INC. (CDXS)·Q2 2025 Earnings Summary