Net Loss to Adjusted EBITDA: Non-GAAP Reconciliations Three Months Ended December 31 Year Ended December 31 $ in Thousands 2020 2019 2020 2019

Nature Inspired. Technology Driven.™ FOURTH QUARTER 2020 FINANCIAL RESULTS CONFERENCE CALL, MARCH 4, 2021

We have made these forward-looking statements in reliance on the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. In some cases, you can identify these statements by forward-looking words such as “anticipates,” “believes,” “continue,” “estimates,” “expects,” “targets,” “intends,” “may,” “might,” “plans,” “potential,” “predicts,” “projects,” “should,” “will,” or the negative of these terms and other similar terminology. Forward-looking statements in this report include statements about the potential impact of the COVID-19 pandemic on our business and operating results; our future financial performance; product pipeline and development; our business model and strategies for commercialization and sales of commercial products; regulatory progression; potential collaborations, partnerships and licensing arrangements and their contribution to our financial results, cash usage, and growth strategies; and anticipated trends in our business. These and other forward-looking statements are predictions and projections about future events and trends based on our current expectations, objectives and intentions and premised on current assumptions. Our actual results, level of activity, performance, or achievements could be materially different than those expressed, implied, or anticipated by forward-looking statements due to a variety of factors, including, but not limited to: the severity and duration of the evolving COVID-19 pandemic and the resulting impact on macro-economic conditions; the impact of increased competition; disruptions at our key facilities; changes in customer preferences and market acceptance of our products; competition for collaboration partners and licensees and the successful execution of collaborations and licensing agreements; the impact of adverse events during development, including unsuccessful field trials or developments trials or disruptions in seed production; the impact of improper handling of our product candidates by unaffiliated third parties during development, such as the improper aerial spraying of our high fiber wheat product candidate; failures by third-party contractors; inaccurate demand forecasting; the effectiveness of commercialization efforts by commercial partners or licensees; our ability to make grain sales on terms acceptable to us; the timing of our grain sales; our ability to collect accounts receivable; disruptions to supply chains, including transportation and storage functions; commodity price conditions; the impact of changes or increases in oversight and regulation; disputes or challenges regarding intellectual property; proliferation and continuous evolution of new technologies; management changes; dislocations in the capital markets; and other important factors discussed in Part I, Item 1A, “Risk Factors” of this Annual Report on Form 10-K, which should be considered an integral part of Part II, Item 7, “Management’s Discussion and Analysis of Financial Condition and Results of Operations.”

Dr. Ribeill has served as a member of the Calyxt board since July 2018 and was Calyxt's interim Chief Executive Officer from August 2018 to October 2018. Since January 2018, he has served as the Chief Executive Officer of Ribogenics, Inc., which is a private biotechnology company working on RNA biology. Dr. Ribeill was also a founder of SCYNEXIS, Inc. (SCYX) and served as its Chief Executive Officer from November 1999 to April 2015. Dr. Ribeill has more than 35 years of experience in the healthcare industry, with an expertise in anti-infective diseases. Prior to moving to the U.S. 21 years ago, Dr. Ribeill held several management positions during his international career with Rhône-Poulenc and Aventis in France Yves Ribeill, Ph.D. and in the UK. Dr. Ribeill was a member of the Scientific Advisory Committee of the World Health Organization and the Medicines for Malaria Venture in Geneva.

• Leveraging differentiated technology to develop product candidates including TALEN® gene-editing platform

• First to bring gene-edited consumer trait to market

1 • Pipeline has total addressable market of $8.8 billion and is targeted at critical industry dynamics including consumer demand for specialty ingredients and supporting sustainability objectives

• Capital-efficient business model with multiple routes to market for product candidates

1 See the information on slides 47-52 of Calyxt’s 2020 Virtual Investor Day on November 17, 2020 available on the Company’s website for sources and key assumptions underlying the total addressable market and potential product revenue opportunities, which includes information that was publicly disclosed as of November 17, 2020 and is not being updated as of the date of this presentation. © CALYXT, INC. ALL RIGHTS RESERVED 4 Q4 2020 Key Highlights • Continued development of key projects in oats and hemp, and carried on our development in soybean, extending our first-mover advantage in this broad-acre crop

• Secured commitment from ADM (NYSE: ADM) to purchase all remaining 2019 grain inventory and 2020 grain production o Key step in Calyxt’s transition to advanced go-to-market strategies o Expected cumulative sales of over 4 million bushels o As of this date all 2019 grain inventory and 40 percent of 2020 grain production has been sold; sales will continue throughout 2021

• Executed commercial agreement with S&W Seed Company (NASDAQ: SANW) for the exclusive license of IQ™ Alfalfa seed in the U.S. and other select geographies

• Capital raise completed, contributing to extension of cash

• Entered into a soybean seed sale agreement with Perdue AgriBusiness

• Yves Ribeill, Ph.D. named Executive Chairman, replacing CEO Jim Blome

• Completed appointments of world-renowned plant- biochemistry experts to new Scientific Advisory Board o Dan Voytas, Ph.D., Calyxt Scientific Advisory Board Chair and Professor in the Department of Genetics, Cell Biology and Development at the University of Minnesota o Anne Osbourn, Ph.D., Group Leader at the John Innes Center o Elizabeth Sattely, Ph.D., HHMI Investigator and Associate Professor of Chemical Engineering, Stanford University o Paul Bernasconi, Ph.D., Former Global Function Head for Molecular Biology at BASF Biosciences

Go-To-Market Initiation Development Commercial Strategy

Trait Development & Upfront fee based on Annual or Milestone- Royalties on commercial Licensing size of opportunity based fees product / value

Seed -- -- Revenue from sales Sales

Technology Upfront fee based on Royalties on commercial Annual fees Licensing size of opportunity product / value

© CALYXT, INC. ALL RIGHTS RESERVED 7 Prioritized Development Pipeline NINE PROJECTS REPRESENT AN $8.8B ADDRESSABLE MARKET Target Commercial Target GTM Partner Addressable Crop Trait Planting Year1 Strategy Status Market1

($ in millions)

Alfalfa Improved digestibility 2021 Trait $65

Wheat High fiber 2023 Trait Prospecting $190

Soybean High oleic, low linolenic (HOLL) 2 2023 Seed Prospecting $7602

Seed Hemp Marketable yield 2023 Prospecting Trait $2,100 Seed Hemp Low THC for fiber, food, & nutraceutical 2024 Prospecting Trait Seed Oat Winter (cold tolerant) 2026 Prospecting $3,600 Trait Seed Soybean Improved HOLL2 2026 Trait Seed Soybean High saturated fat 2026 Prospecting Trait $2,100

Soybean Enhanced protein flavor 2027 Trait

We are also negotiating with potential partners with respect to specific opportunities for which development activity would only commence upon reaching an agreement. $8,800 1 See the information on slides 47-52 of Calyxt’s 2020 Virtual Investor Day on November 17, 2020 available on the Company’s website for sources and key assumptions underlying the total addressable market and potential product revenue opportunities, which includes

information that was publicly disclosed as of November 17, 2020 and is not being updated as of the date of this presentation. © CALYXT, INC. ALL RIGHTS RESERVED 8 2 The $760 million represents the aggregated value of all HOLL seed projects’ addressable market Fourth Quarter Financial Results

Three Months Ended December 31

$ in millions except per share amounts 2020 2019 Revenue $ 13.9 $ 3.8 Gross margin, as reported $ (4.9) $ (1.7) Gross margin (%) (35%) (44%) Gross margin, as adjusted¹ $ (3.9) $ (1.6) Gross margin, as adjusted (%)¹ (28%) (43%) Operating expenses $ 8.1 $ 10.3 Net loss $ (13.4) $ (12.2) Adjusted net loss¹ $ (12.0) $ (12.0) Net loss per share $ (0.37) $ (0.37) Adjusted net loss per share¹ $ (0.33) $ (0.37) Adjusted EBITDA¹ $ (9.8) $ (8.6)

¹ Gross margin, as adjusted and adjusted net loss, net loss per share, and adjusted EBITDA are non-GAAP measures. Reconciliations are provided to gross margin, net loss, and net loss per share, the associated GAAP measures, beginning on page 19 of this presentation. © CALYXT, INC. ALL RIGHTS RESERVED 9 Fourth Quarter Cash Usage Bridge NET CASH USED IN THE FOURTH QUARTER OF 2020 IMPROVED BY $17.6 MI LLI ON COMPARED TO THE FOURTH QUARTER OF 2019 $ in Millions

Year Ended December 31

$ in millions except per share amounts 2020 2019 Revenue $ 23.9 $ 7.3 Gross margin, as reported $ (11.3) $ (2.0) Gross margin (%) (47%) (27%) Gross margin, as adjusted¹ $ (7.2) $ (4.5) Gross margin, as adjusted (%)¹ (30%) (61%) Operating expenses $ 32.6 $ 37.7 Net loss $ (44.8) $ (39.6) Adjusted net loss¹ $ (40.3) $ (40.5) Net loss per share $ (1.32) $ (1.21) Adjusted net loss per share¹ $ (1.19) $ (1.23) Adjusted EBITDA¹ $ (31.6) $ (29.8)

¹ Gross margin, as adjusted and adjusted net loss, net loss per share, and adjusted EBITDA are non-GAAP measures. Reconciliations are provided to gross margin, net loss, and net loss per share, the associated GAAP measures, beginning on page 27 of this presentation. © CALYXT, INC. ALL RIGHTS RESERVED 11 Annual Cash Usage Bridge NET CASH USED IN 2020 INCREASED BY $6.4 MILLION COMPARED TO 2019

$ in Millions

December 31, 2020 cash, cash equivalents, restricted cash, and short-term investments were $30.0 million. © CALYXT, INC. ALL RIGHTS RESERVED 12 2021+ Business Milestone Targets GOAL: UNDERPIN ROAD MAP TO SUCCESS OVER THE NEXT 2 YEARS

Advance Advance Advance Plant- Advance Advance High Sat Fat IQ™ Alfalfa based protein to Winter Oat to Hemp to Soy to to Phase 3 Phase I Phase 2 Phase 2 Phase 2

2021 2022 2023

Sign HFW Advance Secure HOLL Soy Partner HOLL Soy to Seed Purchasers Phase 3 Pilot Launch of IQ™ Secure HO Soy Alfalfa Seed Purchasers

COMPANY OVERVIEW KEY HIGHLIGHTS • Calyxt is a technology company focused • New commercial agreement with S&W Seed on delivering plant-based innovations to Company marks first trait license agreement end users across industries including food, • Commitment for purchase of all 2020 grain production agriculture, nutraceuticals, and energy by ADM and overall transition on track for late 2021 completion • Leader in gene editing • Actively negotiating development agreements with • Robust IP portfolio potential partners • Product pipeline comprised of 9 projects at Phase I or later in development across alfalfa, hemp, oats, soybean and wheat • Pipeline has total addressable market of $8.8 billion1 • Cash of $30.0M as of December 31, 2020, and a runway into second half of 2022

1 See the information on slides 47-52 of Calyxt’s 2020 Virtual Investor Day on November 17, 2020 available on the Company’s website for sources and key assumptions underlying the total addressable market and potential product revenue opportunities, which © CALYXT, INC. ALL RIGHTS RESERVED 14 includes information that was publicly disclosed as of November 17, 2020 and is not being updated as of the date of this presentation. FINAL REMARKS AND Q&A

Calyxt, Inc. Share price $9.65 2800 Mount Ridge Road Roseville, MN 55113 Market cap $357.7M www.calyxt.com Shares outstanding 37.1M

Public float 13.8M

Investor Relations Insider holdings 72.4%

Chris Tyson As of March 1, 2021 Executive Vice President – MZ North America This chart includes information that was publicly Direct: 949-491-8235 disclosed as of the dates above and is not being [email protected] updated as of the date of this presentation. www.mzgroup.us

CLXT News Releases NASDAQ Listed • Calyxt to Present at Upcoming March Investor Conferences – March 3, 2021 Shares Outstanding: 37,065,0441 • Calyxt Announces Completion of New Scientific Advisory Board – March 2, 2021 February 23, 1 • Calyxt Announces High Oleic Soybean Seed Sales Agreement with Perdue AgriBusiness - Options/Warrants: 5,522,418 2021 Agricultural Sector: • Calyxt Announces Dr. Yves Ribeill Appointed As Executive Chair Replacing CEO Jim Technology Blome - February 19, 2021 Year-End: December 31 • Calyxt Announces Sale of Entire 2020 Grain Production to ADM - December 14, 2020 • Calyxt Announces Collaboration with NRGene® to Advance its Product Pipeline - November 11, 2020 Sell-Side Analyst Coverage • Calyxt Announces Commercial Agreement with S&W Seed Company to Deliver Berenberg Donald McLean Improved Quality Alfalfa - October 29, 2020 Canaccord Genuity Bobby Burleson • Calyxt Announces $15 Million Registered Direct Offering - October 16, 2020 H.C. Wainwright Amit Dayal • Calyxt Appoints Sarah Reiter as Vice President of Business Development – October 14, 2020 Jefferies Laurence Alexander Ladenburg Thalmann Robert Leboyer Upcoming Events National Securities Ben Klieve • BofA Securities Global Agriculture and Materials Conference – March 3, 2021 • ROTH Virtual Conference – March 16, 2021

1 As of December 31, 2020 • Investor Summit: Q1 Virtual Summit – March 23-25, 2021 Note: Calyxt, Inc. is followed by the analysts listed above. Please note that any opinions, estimates or forecasts regarding Calyxt, Inc.'s performance made by these analysts © CALYXT, INC. ALL RIGHTS RESERVED 17 are theirs alone and do not represent opinions, forecasts or predictions of Calyxt, Inc. or its management. Calyxt, Inc. does not by its reference above or distribution imply its endorsement of or concurrence with such information, conclusions or recommendations. The above table also includes information that was publicly disclosed as of the dates above and is not being updated as of the date of this presentation. APPENDIX

To supplement our audited financial results prepared in accordance with GAAP, we have prepared certain non-GAAP measures that include or exclude special items. These non-GAAP measures are not meant to be considered in isolation or as a substitute for financial information presented in accordance with GAAP and should be viewed as supplemental and in addition to our financial information presented in accordance with GAAP. Investors are cautioned that there are material limitations associated with the use of non-GAAP financial measures. In addition, other companies may report similarly titled measures, but calculate them differently, which reduces their usefulness as a comparative measure. Management utilizes these non-GAAP metrics as performance measures in evaluating and making operational decisions regarding our business.

We present adjusted gross margin, a non-GAAP measure that includes the effects of Grain Costs expensed as R&D in a prior period, excludes the effects of commodity derivatives entered into to hedge the change in value of fixed price grain inventories and fixed price Forward Purchase Contracts as the expected impact from these contracts will be fully offset when the underlying grain is sold, and excludes the impact of any net realizable value adjustments to inventories occurring in the period, which would otherwise have been recorded as an adjustment to value in a prior period or would have been recorded in a future period as the underlying products are sold.

We present adjusted net loss, a non-GAAP measure, and define it as net loss including the effects of Grain Costs expensed as R&D in a prior period, and excluding the effects of commodity derivatives entered into to hedge the change in value of fixed price grain inventories and fixed price Forward Purchase Contracts as the expected impact from these contracts will be fully offset when the underlying grain is sold, any net realizable value adjustments to inventories occurring in the period, which would otherwise have been recorded as an adjustment to value in a prior period or would have been recorded in a future period as the underlying products are sold, Section 16 officer transition expenses, R&D payroll tax credits that are no longer realizable, restructuring costs, the recapture of non-cash stock compensation expense from the forfeiture and modification of unvested stock awards associated with staffing adjustments made as part of the advancement of our soybean business model, and non-operating expenses, which are primarily gains and losses on foreign exchange transactions and losses on the disposals of land, building, and equipment.

We present adjusted net loss per share, a non-GAAP measure, and define it as net loss per share including the effects of Grain Costs expensed as R&D in a prior period, and excluding the effects of commodity derivatives entered into to hedge the change in value of fixed price grain inventories and fixed price Forward Purchase Contracts as the expected impact from these contracts will be fully offset when the underlying grain is sold, any net realizable value adjustments to inventories occurring in the period, which would otherwise have been recorded as an adjustment to value in a prior period or would have been recorded in a future period as the underlying products are sold, Section 16 officer transition expenses, R&D payroll tax credits that are no longer realizable, restructuring costs, the recapture of non-cash stock compensation expense from the forfeiture and modification of unvested stock awards associated with staffing adjustments made as part of the advancement of our soybean business model, and non- operating expenses, which are primarily gains and losses on foreign exchange transactions and losses on the disposals of land, buildings, and equipment.

We present adjusted EBITDA, a non-GAAP measure and define it as net loss excluding interest, net, income tax expense, depreciation and amortization expenses, stock-based compensation expenses, the effects of commodity derivatives entered into to hedge the change in value of fixed price grain inventories and fixed price Forward Purchase Contracts as the expected impact from these contracts will be fully offset when the underlying grain is sold, any net realizable value adjustments to inventories occurring in the period, which would otherwise have been recorded as an adjustment to value in a prior period or would have been recorded in a future period as the underlying products are sold, Section 16 officer transition expenses, R&D payroll tax credits that are no longer realizable, restructuring costs, and non-operating expenses, which are primarily gains and losses on foreign exchange transactions and losses on the disposals of land, buildings, and equipment; and including the effects of Grain Costs expensed as R&D in a prior period.

Reconciliations Three Months Ended December 31 Year Ended December 31

$ in thousands 2020 2019 2020 2019

Gross margin (GAAP measure) $ (4,936) $ (1,651) $ (11,276) $ (1,984)

Gross margin percentage (35%) (44%) (47%) (27%)

Adjustments:

Grain costs expensed as R&D — — — (3,349)

Unrealized mark-to-market loss 1,694 — 2,801 —

Net realizable value adjustment to inventories (678) 37 1,322 869

Adjusted gross margin $ (3,920) $ (1,614) $ (7,153) $ (4,464)

Adjusted gross margin percentage (28%) (43%) (30%) (61%)

We provide in the table above a reconciliation of adjusted gross margin to gross margin, which is the most directly comparable GAAP financial measure. We provide adjusted gross margin because we believe that this non-GAAP financial metric provides investors with useful supplemental information at this stage of commercialization as the amounts being adjusted affect the period-to-period comparability of our gross margins and financial performance.

Net loss (GAAP measure) $ (13,395) $ (12,165) $ (44,836) $ (39,612)

Non-GAAP adjustments:

Grain costs expensed as R&D — — — (3,349)

Unrealized mark-to-market loss 1,694 — 2,801 —

Net realizable value adjustment to inventories (678) 37 1,322 869

Section 16 officer transition expenses 50 117 543 1,169

Research and development payroll tax credit — — — 410

Restructuring costs 249 — 685 —

Recapture of non-cash stock compensation (75) — (981) —

Non-operating expenses 126 49 126 49

Adjusted net loss $ (12,029) $ (11,962) $ (40,340) $ (40,464)

We provide in the table above a reconciliation of adjusted net loss to net loss, which is the most directly comparable GAAP financial measure. We provide adjusted net loss because we believe that this non-GAAP financial metric provides investors with useful supplemental information at this stage of commercialization as the amounts being adjusted affect the period-to-period comparability of our net losses and financial performance. © CALYXT, INC. ALL RIGHTS RESERVED 21 Net Loss Per Share: GAAP to Non-GAAP Reconciliations Three Months Ended December 31 Year Ended December 31

$ in thousands 2020 2019 2020 2019

Net loss per share (GAAP measure) $ (0.37) $ (0.37) $ (1.32) $ (1.21)

Non-GAAP adjustments:

Grain costs expensed as R&D — — — (0.10)

Unrealized mark-to-market loss 0.05 — 0.08 —

Net realizable value adjustment to inventories (0.02) — 0.04 0.03

Section 16 officer transition expenses — — 0.02 0.04

Research and development payroll tax credit — — — 0.01

Restructuring costs 0.01 — 0.02 —

Recapture of non-cash stock compensation — — (0.03) —

Non-operating expenses — — — —

Adjusted net loss per share $ (0.33) $ (0.37) $ (1.19) $ (1.23) We provide in the table above a reconciliation of adjusted net loss per share to net loss per share, which is the most directly comparable GAAP financial measure. We provide adjusted net loss per share because we believe that this non-GAAP financial metric provides investors with useful supplemental information at this stage of commercialization as the amounts being adjusted affect the period-to-period comparability of our net losses per share and financial performance. © CALYXT, INC. ALL RIGHTS RESERVED 22 Net Loss to Adjusted EBITDA: Non-GAAP Reconciliations Three Months Ended December 31 Year Ended December 31 $ in thousands 2020 2019 2020 2019

Net loss (GAAP measure) $ (13,395) $ (12,165) $ (44,836) $ (39,612)

Non-GAAP adjustments:

Interest, net 310 186 878 (110)

Depreciation and amortization expenses 497 556 1,869 1,607

Stock-based compensation expenses 1,333 2,610 4,971 9,175

Grain costs expensed as R&D — — — (3,349)

Unrealized market-to-market loss 1,694 — 2,801 —

Net realizable value adjustment to inventories (678) 37 1,322 869

Section 16 officer transition expenses 50 117 543 1,169

Research and development payroll tax credit — — — 410

Restructuring costs 249 — 685 —

Non-operating expenses 126 49 126 49

Adjusted EBITDA $ (9,814) $ (8,610) $ (31,641) $ (29,792) We provide in the table above a reconciliation of adjusted EBITDA to net loss, which is the most directly comparable GAAP financial measure. Because adjusted EBITDA excludes non-cash items and discrete or infrequently occurring items, we believe that adjusted EBITDA provides investors with useful supplemental information about the operational performance of our business and facilitates comparison of our financial results between periods where certain items may vary significantly independent of our business performance. © CALYXT, INC. ALL RIGHTS RESERVED 23