Codexis Corporate PresentationJune 2019

NASDAQ: CDXS

• These slides and any accompanying oral presentation contain forward-looking statements that involve risks and uncertainties. These statements relate to future events or our future

financial or operational performance and involve known and unknown risks, uncertainties and other factors that could cause our actual results or levels of activity, performance or

achievement to differ materially from those expressed or implied by these forward-looking statements. Forward-looking statements include all statements that are not historical facts. In

some cases, you can identify forward-looking statements by terms such as “may,” “will,” “should,” “could,” “would,” “expects,” “plans,” “anticipates,” “believes,” “estimates,” “projects,”

“predicts,” “potential” or the negative of these terms, and similar expressions and comparable terminology intended to identify forward-looking statements. These forward-looking

statements represent our estimates and assumptions only as of the date hereof, and, except as required by law, we undertake no obligation to update or revise publicly any forward-

looking statements, whether as a result of new information, future events or otherwise.

• Other factors that could materially affect actual results or levels of activity, performance or achievement can be found in Codexis’ Form 10-K for the period ended December 31, 2018

filed with the SEC on March 1, 2019 and the Form 10-Q filed on May 8, 2019, including under the caption “Risk Factors,” and Codexis’ other current and periodic reports filed with the

SEC. If any of these risks or uncertainties materialize, or if our underlying assumptions prove to be incorrect, actual results or levels of activity, performance or achievement may vary

significantly from what we projected.

• Our logo, “Codexis,” “CodeEvolver®,” and other trademarks or service marks of Codexis, Inc. appearing in this presentation are the property of Codexis, Inc. This presentation contains

additional trade names, trademarks and service marks of other companies. We do not intend our use or display of other companies’ trade names, trademarks or service marks to imply

relationships with, or endorsement or sponsorship of us by, these other companies.

Forward Looking Statements

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Codexis: What We Do

Wielding a leading edge protein engineering platform technology, CodeEvolver®, AI powered, and constantly accelerating

Dramatically enhancing proteins to deliver unique and value-creating performance

In partnership with some of the world’s most innovative companies, in a growing list of industries

Driving sustainable financial growth, based on multiple revenue generation models, working in parallel

Proteins – Infinite Source of New Value Creating Materials

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Core Challenge 1: How To Drive Protein Function?

DNA Code Protein Sequence Protein Function

Codexis Uniquely Mapping This Big Data Landscape

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CodeEvolver®: Leading Protein Engineering Platform

Starting Proteinfrom nature, Codexis libraries,

or in silico designed

Computer modeling & AI-driven structure-function mapping

deeply mines vast data generated; increasinglypredictive of real world protein performance

Diverse libraries of novel enzymes

designed, created &

sequencedin a highly

automated workflow

Automated Performance

Analysesin precise bio-

chemical assays to assess actual

function and performance

CodeEvolver® Engineered Protein

tailored for specific end use application

~500,000 protein variants designed, produced, performance-tested, and sequenced in 2018

For more on CodeEvolver®

https://youtu.be/xSW0UDIgWRI

https://youtu.be/up5QUdTLsBU

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With Accelerating Speed & Shrinking R&D Costs

40Scientists Years

Per Project

10Scientists Years

Per Project

2Scientists Years

Per Project

Continued

Acceleration

Sources of CodeEvolver®’s Acceleration

✓ Expanding libraries of better-performing starter proteins

✓ Increasingly fast, automated HTP protein production and performance testing

✓ Proprietary AI algorithms predicting protein function more accurately

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Core Challenge #2: What World Challenges Can Proteins Solve?

CodeEvolver®Engineered

Protein

Beginning Protein CodeEvolver®+ =

Performance& Cost Targets

DesiredReal World

Function

Collaborate with World’s Leading InnovatorsClient’s Market Knowledge w/ Codexis Protein Experts

Protein’s Blueprint:

• Activity

• Stability

• Immunogenicity

• Developability

• Manufacturability

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Codexis: Impacting a Growing List of Real World Markets

Protein Catalysts for Pharma Manufacturing

Novel, High Performing Industrial Enzymes

History: First non-pharma project 2014

Status: Food Ingredients → Diagnostics → …

TAM: $6+ bn2 industrial enzymes

Biotherapeutics

History: 1st target starts 2014; expanded 2017

Status: 1 Clinical + 5 Preclinical Programs

TAM: $6+ bn1 enzyme therapeutics

History: Codexis making the market for 16+ yrs

Status: Business w/ 21 of Top 25 Pharma Companies

TAM: $1+ bn3 can improve > ⅓ of all small molecule drugs

1) BCC Research Report BIO021E, May 2016 2) Research and Markets Report 4331705, June 2017 3) Codexis estimates

Novel BiotherapeuticsMonetize via R&D partnering

& outlicensing

Performance EnzymesMonetize via R&D partnering& commercial enzyme sales

Two reported segments

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Performance Enzymes: Pharma Manufacturing

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Protein Catalysts For Green Pharmaceutical Manufacturing

CodeEvolver®Engineered

Protein

Beginning Protein CodeEvolver®+ =

Protein Catalyst Process Benefits

• Lower impurities

• Higher yields

• Fewer process steps

• Atmospheric, CMO portable

• Less waste

• Energy efficient

Collaborating with 21 of Top 25 Pharma Companies (plus many smaller pharma companies)

14 Phase II / III Installations (doubled in last two years)

+ 12 On-Market Drug Processes: 8 commercial installations + 4 under development+ 3 of Top 10 Pharma Companies licensed CodeEvolver® to create proteins on their own

Collaborators

16+ year history of demanding targets → sharpens CodeEvolver®

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Innovative Partnerships with Global Pharma Leaders

Increased Codexis access of smaller pharmaceutical companies

Porton larger RFP pipeline → new opportunity touches for Codexis

Porton rapid screening → increase Codexis installation prospects

Limited, leveraged Codexis cost of sales per $ of revenue

Porton potential to manufacture → increase value share to CDXS

For each1 licensee created protein:

CDXS eligible to receive between $5.75m to $38.5m in milestones

CDXS eligible to earn volumetric ‘per kg of API’ royalties

up to a cap of $15m

CDXS eligible to earn volumetric ‘per kg of API’ royalties -

No cap

Technology transfer3Q14 – 2Q’16

Upfront + milestones: $25m

Technology transfer3Q’15 – 4Q’16

Upfront + milestones: $18m

Technology transfer2Q’19 – 1Q’21

Upfront + milestones +Improvements license: $22m

Back-end EconomicsFront-end EconomicsAcquire license & training

Backend Payments Outlook

• 100% margin, 7-digit backend payments expected to begin in 2019

• With time, 100% margin annuities will stack and grow

Strategic Channel Partnership

“Nearly 80% of the products approved by the FDA on behalf of

small pharma companies are contract manufactured”2

CodeEvolver® Platform Licensees

Partnership Success Catalysts:

• Finalize screening tech transfer

• Porton projects shown on Codexis annual pipeline

• Porton directs CodeEvolver® team

• Porton invests in enzyme mfr

Validate the applicability of CodeEvolver® to enable

improvements on long term list of APIs’ manufacturing

Invest to run CodeEvolver® on their own

1) Subject to certain negotiated limitations, which vary by licensee 2) PharmTech, “What’s Next for the CMO Industry,” Jim Miller, Aug 2, 2016

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Performance Enzymes: Industrial Enzymes

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Food: Innovative Partnership Tackles Better Tasting Stevia

CodeEvolver®Engineered

Protein

Beginning Protein CodeEvolver®+ =

Enzyme Cascade’s Blueprint:

• Multiple enzyme step conversion

• Optimize all in tandem: activity, selectivity, substrate load, co-factor use

• High thermal stability

• Very low enzyme cost-in-use

Reb M Cascade Nails The Blueprint!

✓ Started end-2016 → GRAS filed mid-2018

✓ >200,000 variants produced and tested

✓ 80-100+ sequence changes for each enzyme

✓ High: titer / yield / cofactor recycle

✓ One-pot scheme w/ simple downstream

Ideal sweetener: taste of sugar, non-caloric, natural

Stevia (‘Reb A’) bitter taste severely limits its use

Trace Reb M in leaf identified having taste near sugar

Reb M supply unavailable; costs out of line

Fermentation routes to Reb M – slow to commercialize

Reb A

Steviol

G

GG

G

Reb M

Steviol

G

GG

G

G

G

EnzymeCascade

Leafextraction

Stevia LeafWater Wash

Drier

Leaf extract, enzymes, etc.

>95% pure Reb M

Collaborator

✓ T&L introduces Tasteva®M to market in 3Q’18

✓ ‘Strong early customer interest’Nick Hampton, T&L CEO, earnings webcast Nov 8, 2018

✓ Expect to become a top CDXS product with time

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Multi-year Commercial Agreement signed in April 2019

MDx: Improved DNA Ligase For Next Generation Sequencing

CodeEvolver®Engineered

Protein

Beginning Protein CodeEvolver®+ = 0%

20%

40%

60%

80%

100%

0 5 10 15 20 25 30

Do

ub

le-l

igat

ed c

on

vers

ion

Time (min)

Ligation time-course, 40nM adapterFirst Enzyme’s Blueprint:

• Ligation conversion – activity & sensitivity

• Effective at trace DNA input levels

• Rapid rate of ligation

• Minimize/eliminate need for PEG

• Workflow and NGS machine agnostic

Enzymes are Core to NGS Workflows:

Library Prep Data AnalysisNGS RunSample Prep AmplificationSample Isolation Library Quant Interpretation

Target: Improve the enzymes to enable more sensitive,

high fidelity NGS diagnostic tests → earlier,

less invasive cancer detection

Codexis Ligase

T4 DNA Ligase

Codexis MDx Product Launches✓ Fast growing, $600m1 enzyme target market

✓ First Codexis MDx enzyme – Evo T4 DNA Ligase:

• At AMP2, NGS leader publicizes 20-50% coverage increases at low (10-50 ng) DNA concentrations

✓ Strategic partnering discussions are underway

✓ Second MDx enzyme – DNA polymerases near launch

• Largest enzyme class used in the MDx market

1) Markets and Markets Report BT 2612, Oct 20172) Association of Molecular Pathologists, San Antonio, Nov 2018

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~ $6+ Billion1

Industrial Enzyme

Sectors

Chemicals & Energy Animal Feed & Health Flavors and Fragrances

Detergents Molecular Diagnostics & Biology

Food and Nutrition

Extending CodeEvolver® Reach Into More Industrial Verticals

1) Research and Markets Report 4331705, June 2017

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Novel Biotherapeutics

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First Clinical Drug Candidate: Oral Enzyme For Phenylketonuria (PKU)

CodeEvolver®Engineered

Protein

Beginning Protein CodeEvolver®+ =

Protein digestion:• Trypsin• Chymotrypsin• CarboxypeptidaseAmino acid uptake

Protein’s Blueprint:

• Highly active on phenylalanine, and not on tyrosine

• Stable; easy to manufacture

• Tolerant to low pH in stomach

• Resistant to proteolytic degradation in small intestine

CDX-6114 Hits The Blueprint!

0 2 4 6

0

5 0 0

1 0 0 0

1 5 0 0

2 0 0 0

2 4 2 6 2 8 3 0 4 8 5 0 5 2 5 4

T im e (h rs )

Pla

sm

a C

A (

ng

/mL

)

D a y 1 D a y 2 D a y 3

Preclinical Proof-of-conceptCollaborator

1) ClinicalTrials.gov: NCT 03577886

2) Topline results reported by Codexis on November 8, 2018

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Phase 1a – Single Ascending Dose Clinical Trial1, 2

32 healthy volunteers in four cohorts

Safety & tolerability demonstrated across entire dose range

No serious adverse events or GI-related symptoms observed

Pharmacokinetics readout: no evidence of systemic exposure

Dose-dependent pharmacodynamic response observed

Innovative Partnership w/Nestlé Health Science (NHSc)

NHSc and Codexis Biotherapeutic Development Collaboration (Oct. 2017)

✓ Granted exclusive option to Nestlé to license oral PKU drug candidate CDX-6114

o $14m upfront + $4m milestone + $1m solid dose milestone collected to-date

o NHSc option exercise decision (1Q’19) - $3m milestone earned

o Opportunity for up to $85m add’l pre-commercial and $250m commercial milestone payments

o Plus, tiered royalties on sales ranging from mid-single-digit % to low-double-digit %

✓ Granted first-look rights to Nestlé to other IEAAM pipeline programs

✓ NHSc funds Codexis to discover novel enzyme for a new disease target

“The partnership with Codexis strengthens our footprint in the enzyme field, a fast-developing part of the nutritional therapy innovation frontier that is changing the way we manage our health.”1

—Greg Behar, President, Nestlé Health Science

1) Nestlé Health Science Press Release, October 12, 2017

CDX-6114

Codexis’ 1st successful biotherapeutic clinical trial

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Codexis Novel Biotherapeutic Pipeline

CodeEvolver®-generated in vitro Candidate Discovery

Preclinical Research IND Enabling Clinical Trials

CDX-6114: Inborn Error of Amino Acid Metabolism (IEAAM) - PKU

IEAAM # 3

LSD #2

Discovery Partnership

Drug Target 1 (DT1)Lysosomal Storage Disease (LSD) #1

IEAAM # 2

2 additional partnerableassets projected in 2019

PLUS: prospects for other new discovery partnering deals targeting modalities beyond enzyme therapeutics

NHSc option exercised

CDX-6114 for PKUPhase 1a: Met all defined

endpoints (Nov 2018)

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Financial Highlights

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2018 Full Year ResultsFifth Consecutive Year of Building Momentum for Codexis

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2018 R&D Revenue

+50% vs 2017

$35.0m

2018 Total Revenue

+21% vs 2017

$60.6m✓ Step-out Y-O-Y Revenue Expansion on Top of Solid Pharma Mfr Base

• Performance Enzymes→ Pharma Mfr $39.2m +7%

• Performance Enzymes → Non-Pharma $7.9m +39%

• Novel Biotherapeutics $13.5m +76%

✓ Strategic Deliverables in Performance Enzymes

• Commercialized enzymes for Tate & Lyle stevia sweetener in < 2yrs

• Eight pharma customers with revenues > $1m (+33% from six in 2017)

• Porton partnership expands customer access: deal to $2.8+ rev in < 1yr

• Breaking into MDx: DNA Ligase first revs; DNA Polymerase poised

✓ Novel Biotherapeutic Segment Credibly Established

• Successfully completed company’s first-ever clinical trial – CDX-6114 for PKU

• Phase 1a and solid dose formulation results→ Nestlé's 1Q’19 opt-in

• 5 more BioTx programs advance towards partnerable events

✓ One of Nation’s Best & Brightest Firms to Work For – 2nd Yr in Row

✓ Ends Year with Strengthened Balance Sheet: $50m+ Cash; No Debt

Performance vs Annual Guidance

Fifth Consecutive Year

2018 Product Margin

Up From 46% in 2017

51%

2018 Strategic Deliverables

✓ Met

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Total Revenues: $69 - 72m (+14-19% vs 2018)

Product Sales: $26 - 29m (2018 = $25.6m)

Product Gross Margin: 48 - 52% (2018 = 51%)

Codexis 2019 Financial Outlook

Revenues: ~ 40% in 1H’19 / ~ 60% in 2H’19

R&D + SG&A Expenses: ~ $18m/qtr; ~ Smooth Quarterly

Additional Insights Into 2019 Financial Outlook

Total Revenue ($ million) 2019 Annual Guidance Metrics *

$35

$42

$49$50

$61

$69

$20

$30

$40

$50

$60

$70

$80

2014 2015 2016 2017 2018 2019F

$72

* Originally provided 2/26/19; upheld 5/6/19

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2019 Strategic ObjectivesContinue Business Acceleration on Multiple Fronts

Relentless Focus on CodeEvolver®, AI-Driven Acceleration of Protein Discoveries

✓ Reinforce our powerful, product-commercializing uniqueness in the world’s growing synthetic biology landscape

Significant Acceleration of Announceable Deal Flow Underpins Another Solid Double Digit Revenue Growth Year

✓ Growth in new R&D partnering deals across both segments → new application verticals & clients

✓ Continued widening and deepening of major pharma relationships, and the beginning of CodeEvolver® licensing backend sales

✓ Continued advancement of Performance Enzyme pipeline → growth of both pre-commercial and commercial installations

✓ The year, we will make our mark in establishing growing, profitable sales in molecular diagnostic markets

✓ More than offsetting y-o-y headwinds: Tate & Lyle stevia (2019 prod sales < 2018 R&D revs); Nestlé Health Sciences CDX-6114

Break-out Progress for Novel Biotherapeutics Pipeline

✓ Expect two of the five programs (beyond PKU) will reach partnerable status (locked and on way to IND) by the end of 2019

Smart Spending Investments Enable Growth Acceleration in 2019 & Beyond

✓ Growth in R&D headcount and external spending to accelerate Novel Biotherapeutic pipeline advancement towards IND

✓ Additional R&D hiring to enable expanded protein discovery capacity for growth in partner-funded programs

✓ Impacts of revenue growth and spending investments largely offset each other on bottom-line and cash balance y-o-y

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Unlock the power of proteinsTM

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Contact Us

John NicolsPresident & Chief Executive Officer

• john.nicols@codexis.com

• (650) 421-2388

Gordon SangsterSenior Vice President & Chief Financial Officer

• gordon.sangster@codexis.com

• (650) 421-8115

Jody CainLHA Investor Relations

• jcain@lhai.com

• (310) 691-7100

Corporate Headquarters200 Penobscot Drive

Redwood City, CA 94063

USA

Nasdaq: CDXS

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Appendix – Most Recent Pipeline Snapshot

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Codexis Pipeline Snapshot (June 2018)

Pipeline Project Category

Pre-Commercial CommercialPipeline Total

06/30/2018

vs. prior pipeline

6/30/17

Codexis Driven Sustaining Revenues

CodexisSelf-funded

CustomerPartnered

Product Sales and/or Licensing

Performance Enzymes Improving Pharmaceutical Manufacturing

Developmental Drugs in Clinical Phases II or III 14 n.a. 14 + 4

Patented On-the-Market Drugs 1 2 3 -

Generic On-the-Market Drugs 1 2 6 9 -

Performance Enzymes for Other Industrial Verticals

Food & Nutrition 3 1 4 -

Molecular Diagnostic / Molecular Biology Enzymes 3 3 + 2

Other Industrial Enzymes 1 1 + 1

Novel Biotherapeutics Discovery & Development 7 2 9 + 3

Pipeline Total as of June 30, 2018 11 23 9 43 + 10

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Row Headers

• Independent categories in which Codexis is creating protein innovations that can liberate value-in-use

• Excludes the many projects or product sales for pharmaceutical manufacturing prior to and through Phase 1 development, or which are not clearly confirmed by the customer as being in Phase II or later.

Column Headers

• ALL Projects are Codexis Driven – projects where protein innovations have been or are being developed by Codexis in-house teams. Any projects being performed independently by CodeEvolver® platform licensees are not included.

• Pre-Commercial are projects that have yet to be fully commercially launched by Codexis and/or our customers

• Commercial projects or products that have been fully commercialized by both Codexis and our customers and are sources of sustained revenues for Codexis

For a Project to Register in our Pipeline

• It must have generated > $100,000 in revenue and/or incurred > $100,000 in costs over the prior 2 years

Guide to Codexis Pipeline Snapshot

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0

3

6

9

12

15

DevelopmentalDrugs in ClinicalPhases II or III

PatentedOn-the-Market

Drugs

GenericOn-the-Market

Drugs

NovelBiotherapeutics

Discovery &Development

Food &Nutrition

MolecularDiagnostic /Molecular

Biology

Other Industries

7

3

7

4 4

1

0

10

3

9

6

4

1

0

14

3

9 9

4

3

1

Pipeline Distribution and Growth by Industrial Category

Jun '16 Jun '17 Jun '18

Codexis Pipeline Trend History

26

0

10

20

30

40

50

Jun '16 Jun '17 Jun '18

6 711

20

26

32

Total Pipeline Growth

33

43

CustomerPartnered

CodexisSelf-funded

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