Green Plains Inc. 10-Q

Item 1. Financial Statements. GREEN PLAINS INC. CONSOLIDATED BALANCE SHEETS (in thousands, except share amounts) September 30, 2025 December 31, 2024 (unaudited) ASSETS Current assets Cash and cash equivalents $ 135,903 $ 173,041 Restricted cash 75,722 36,354 Accounts receivable, net of allowances of $ 84 and $ 80 , respectively 84,942 94,901 Inventories 126,968 227,444 Prepaid expenses and other 16,079 27,138 Derivative financial instruments 6,977 10,154 Total current assets 446,591 569,032 Property and equipment, net of accumulated depreciation and amortization of $ 655,761 and $ 749,593 , respectively 958,262 1,042,460 Operating lease right-of-use assets 59,093 72,161 Deferred income taxes, net 26,521 — Other assets 42,016 98,521 Total assets $ 1,532,483 $ 1,782,174 LIABILITIES AND STOCKHOLDERS' EQUITY Current liabilities Accounts payable $ 90,434 $ 154,817 Accrued and other liabilities 59,076 53,712 Derivative financial instruments 27,709 9,500 Operating lease current liabilities 20,930 24,711 Product financing arrangement 20,895 — Short-term notes payable and other borrowings 45,000 140,829 Current maturities of long-term debt 2,042 2,118 Total current liabilities 266,086 385,687 Long-term debt 306,372 432,460 Operating lease long-term liabilities 39,655 49,190 Carbon equipment liabilities 117,519 17,918 Other liabilities 27,902 22,382 Total liabilities 757,534 907,637 Commitments and contingencies (Note 13) Stockholders' equity Common stock, $ 0.001 par value; 150,000,000 shares authorized; 74,734,161 and 67,512,282 shares issued, and 71,929,102 and 64,707,223 shares outstanding, respectively 75 68 Additional paid-in capital 1,264,553 1,213,646 Retained deficit ( 451,516 ) ( 318,298 ) Accumulated other comprehensive income (loss) ( 13,015 ) 973 Treasury stock, 2,805,059 shares ( 31,174 ) ( 31,174 ) Total Green Plains stockholders' equity 768,923 865,215 Noncontrolling interests 6,026 9,322 Total stockholders' equity 774,949 874,537 Total liabilities and stockholders' equity $ 1,532,483 $ 1,782,174 See accompanying notes to the consolidated financial statements. 5 Table of Contents GREEN PLAINS INC. CONSOLIDATED STATEMENTS OF OPERATIONS (unaudited and in thousands, except per share amounts) Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Revenues $ 508,487 $ 658,735 $ 1,662,831 $ 1,874,774 Costs and expenses Cost of goods sold (excluding depreciation and amortization expenses reflected below) 456,321 580,626 1,566,056 1,750,475 Selling, general and administrative expenses 29,335 26,710 99,852 92,429 Gain on sale of assets, net ( 36,006 ) ( 30,723 ) ( 31,962 ) ( 30,723 ) Depreciation and amortization expenses 24,968 26,070 74,915 69,141 Impairment of assets held for sale — — 10,724 — Total costs and expenses 474,618 602,683 1,719,585 1,881,322 Operating income (loss) 33,869 56,052 ( 56,754 ) ( 6,548 ) Other income (expense) Interest income 1,089 1,737 2,726 5,737 Interest expense ( 47,763 ) ( 10,089 ) ( 70,575 ) ( 25,369 ) Other, net ( 2,673 ) 478 ( 4,227 ) 1,272 Total other income (expense) ( 49,347 ) ( 7,874 ) ( 72,076 ) ( 18,360 ) Income (loss) before income taxes and income (loss) from equity method investees ( 15,478 ) 48,178 ( 128,830 ) ( 24,908 ) Income tax benefit 25,638 825 23,238 769 Income (loss) from equity method investees, net of income taxes 814 ( 366 ) ( 28,302 ) ( 2,384 ) Net income (loss) 10,974 48,637 ( 133,894 ) ( 26,523 ) Net income (loss) attributable to noncontrolling interests ( 952 ) 437 ( 676 ) 1,039 Net income (loss) attributable to Green Plains $ 11,926 $ 48,200 $ ( 133,218 ) $ ( 27,562 ) Earnings per share Net income (loss) attributable to Green Plains - basic $ 0.17 $ 0.75 $ ( 1.99 ) $ ( 0.43 ) Net income (loss) attributable to Green Plains - diluted $ 0.17 $ 0.69 $ ( 1.99 ) $ ( 0.43 ) Weighted average shares outstanding Basic 69,855 63,946 66,826 63,741 Diluted 77,869 71,660 66,826 63,741 See accompanying notes to the consolidated financial statements. 6 Table of Contents GREEN PLAINS INC. CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (unaudited and in thousands) Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Net income (loss) $ 10,974 $ 48,637 $ ( 133,894 ) $ ( 26,523 ) Other comprehensive income (loss), net of tax Unrealized gains (losses) on derivatives arising during the period, net of tax expense (benefit) of $ 4,080 , ($ 121 ), $ 7,619 and $ 2,001 , respectively ( 12,105 ) 338 ( 22,603 ) ( 6,362 ) Reclassification of realized losses on derivatives, net of tax benefit of ($ 1,965 ), ($ 1,890 ), ($ 2,904 ) and ($ 4,122 ), respectively 5,831 6,052 8,615 13,105 Total other comprehensive income (loss), net of tax ( 6,274 ) 6,390 ( 13,988 ) 6,743 Comprehensive income (loss) 4,700 55,027 ( 147,882 ) ( 19,780 ) Comprehensive income (loss) attributable to noncontrolling interests ( 952 ) 437 ( 676 ) 1,039 Comprehensive income (loss) attributable to Green Plains $ 5,652 $ 54,590 $ ( 147,206 ) $ ( 20,819 ) See accompanying notes to the consolidated financial statements. 7 Table of Contents GREEN PLAINS INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (unaudited and in thousands) Nine Months Ended September 30, 2025 2024 Cash flows from operating activities Net loss $ ( 133,894 ) $ ( 26,523 ) Adjustments to reconcile net loss to net cash provided by (used in) operating activities Depreciation and amortization 74,915 69,141 Amortization of debt issuance costs and non-cash interest expense 9,691 1,758 Gain on sale of assets, net ( 31,962 ) ( 30,723 ) Impairment of assets held for sale 10,724 — Inventory lower of cost or net realizable value adjustment 275 10,086 Loss on extinguishment of debt 35,654 1,763 Deferred income taxes ( 20,538 ) ( 2,122 ) Stock-based compensation 13,728 10,162 Loss from equity method investees, net of income taxes 28,302 2,384 Other 8,850 404 Changes in operating assets and liabilities before effects of asset dispositions Accounts receivable 9,955 19,185 Inventories 89,812 12,837 Derivative financial instruments ( 1,763 ) 3,245 Prepaid expenses and other assets 16,615 5,541 Accounts payable and accrued liabilities ( 70,417 ) ( 80,514 ) Current income taxes 4,138 577 Other ( 562 ) ( 197 ) Net cash provided by (used in) operating activities 43,523 ( 2,996 ) Cash flows from investing activities Purchases of property and equipment, net ( 31,864 ) ( 67,825 ) Proceeds from the sale of assets 184,249 48,879 Proceeds from the sale of equity method investment 23,500 — Investment in equity method investees, net ( 4,909 ) ( 15,672 ) Net cash provided by (used in) investing activities 170,976 ( 34,618 ) Cash flows from financing activities Payments of principal on long-term debt ( 132,133 ) ( 61,230 ) Proceeds from short-term borrowings 371,650 544,525 Payments on short-term borrowings ( 467,936 ) ( 528,128 ) Net proceeds from product financing arrangement 20,895 — Payments on extinguishment of non-controlling interest — ( 29,196 ) Payments of transaction costs — ( 5,951 ) Payments of loan fees ( 960 ) ( 1,544 ) Payments related to tax withholdings for stock-based compensation ( 2,047 ) ( 4,604 ) Other financing activities ( 1,738 ) ( 3,060 ) Net cash used in financing activities ( 212,269 ) ( 89,188 ) Net change in cash and cash equivalents, and restricted cash 2,230 ( 126,802 ) Cash and cash equivalents, and restricted cash, beginning of period 209,395 378,762 Cash and cash equivalents, and restricted cash, end of period $ 211,625 $ 251,960 Continued on the following page 8 Table of Contents GREEN PLAINS INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (unaudited and in thousands) Continued from the previous page Nine Months Ended September 30, 2025 2024 Reconciliation of total cash and cash equivalents, and restricted cash Cash and cash equivalents $ 135,903 $ 227,460 Restricted cash 75,722 24,500 Total cash and cash equivalents, and restricted cash $ 211,625 $ 251,960 Supplemental investing activities Assets disposed of in sale $ 150,336 $ 21,358 Less: liabilities relinquished ( 12,101 ) ( 3,456 ) Net assets disposed $ 138,235 $ 17,902 Supplemental disclosures of cash flow Cash paid for income taxes, net $ 1,482 $ 631 Cash paid for interest $ 32,996 $ 25,608 Capital expenditures in accounts payable $ 4,037 $ 6,103 Capital expenditures in carbon equipment liabilities $ 117,519 $ 7,213 Non-cash asset retirement obligation additions $ 16,035 $ 1,460 Issuance of common stock as a result of the Merger $ — $ 5 Non-cash extinguishment of non-controlling interest within additional paid-in capital $ — $ 133,765 See accompanying notes to the consolidated financial statements. 9 Table of Contents GREEN PLAINS INC. NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (unaudited) 1. BASIS OF PRESENTATION, DESCRIPTION OF BUSINESS AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES References to the Company References to “Green Plains” or the “company” in the consolidated financial statements and in these notes to the consolidated financial statements refer to Green Plains Inc., an Iowa corporation, and its subsidiaries. Consolidated Financial Statements The consolidated financial statements include the company’s accounts and all significant intercompany balances and transactions are eliminated. Unconsolidated entities are included in the financial statements on an equity method basis. On January 9, 2024, the transactions contemplated by the Merger Agreement were completed and the company acquired all of the publicly held common units of the partnership not already owned by the company and its affiliates. Refer to Note 3 - Merger and Dispositions included herein for more information. The company also owns a majority interest in FQT, with their results being consolidated in our consolidated financial statements. The accompanying consolidated financial statements are prepared in accordance with GAAP for interim financial information and the instructions to Form 10-Q and Article 10 of Regulation S-X. Because they do not include all of the information and footnotes required by GAAP for complete financial statements, the consolidated financial statements should be read in conjunction with the company’s annual report on Form 10-K for the year ended December 31, 2024, filed with the SEC on February 7, 2025. The unaudited financial information reflects adjustments, which are, in the opinion of management, necessary for a fair presentation of results of operations, financial position and cash flows for the periods presented. The adjustments are normal and recurring in nature, unless otherwise noted. Interim period results are not necessarily indicative of the results to be expected for the entire year. Reclassifications Certain prior year amounts have been reclassified to conform to the current year presentation. These reclassifications did not affect total assets, liabilities or equity, but separately disclose comparable balances of liabilities previously disclosed within other liabilities on the consolidated balance sheets. Use of Estimates in the Preparation of Consolidated Financial Statements The preparation of consolidated financial statements in conformity with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. The company bases its estimates on historical experience and assumptions it believes are proper and reasonable under the circumstances and regularly evaluates the appropriateness of its estimates and assumptions. Actual results could differ from those estimates. Certain accounting policies, including but not limited to those relating to derivative financial instruments and accounting for income taxes, are impacted significantly by judgments, assumptions and estimates used in the preparation of the consolidated financial statements. Description of Business The company operates within two operating segments: (1) ethanol production, which includes the production, storage and transportation of ethanol, distillers grains, Ultra-High Protein and renewable corn oil and (2) agribusiness and energy services, which includes grain handling and storage, commodity marketing and merchant trading for company-produced and third-party ethanol, distillers grains, renewable corn oil, natural gas and other commodities. 10 Table of Contents Cash and Cash Equivalents Cash and cash equivalents includes bank deposits as well as short-term, highly liquid investments with original maturities of three months or less. Restricted Cash The company has restricted cash, which can only be used for funding surety bonds and letters of credit and for payment towards a credit agreement. Restricted cash also includes cash margins and securities pledged to commodity exchange clearinghouses. To the degree these segregated balances are cash and cash equivalents, they are considered restricted cash on the consolidated balance sheets. Revenue Recognition The company recognizes revenue when obligations under the terms of a contract with a customer are satisfied. Generally this occurs with the transfer of control of products or services. Revenue is measured as the amount of consideration expected to be received in exchange for transferring goods or providing services. Sales, value add, and other taxes the company collects concurrent with revenue-producing activities are excluded from revenue. Sales of ethanol, distillers grains, Ultra-High Protein, renewable corn oil, natural gas and other commodities by the company’s marketing business are recognized when obligations under the terms of a contract with a customer are satisfied. Generally, this occurs with the transfer of control of products or services. Revenues related to marketing for third parties are presented on a gross basis as the company controls the product prior to the sale to the end customer, takes title of the product and has inventory risk. Unearned revenue is recorded for goods in transit when the company has received payment but control has not yet been transferred to the customer. Revenues for receiving, storing, transferring and transporting ethanol and other fuels are recognized when the product is delivered to the customer. The company routinely enters into physical-delivery energy commodity purchase and sale agreements. At times, the company settles these transactions by transferring its obligations to other counterparties rather than delivering the physical commodity. Revenues include net gains or losses from derivatives related to products sold while cost of goods sold includes net gains or losses from derivatives related to commodities purchased. Revenues also include realized gains and losses on related derivative financial instruments and reclassifications of realized gains and losses on cash flow hedges from accumulated other comprehensive income or loss. Sales of products are recognized when control of the product is transferred to the customer, which depends on the agreed upon shipment or delivery terms. Shipping and Handling Costs The company accounts for shipping and handling activities related to contracts with customers as costs to fulfill its promise to transfer the associated products. Accordingly, the company records customer payments associated with shipping and handling costs as a component of revenue, and classifies such costs as a component of cost of goods sold. Cost of Goods Sold Cost of goods sold includes materials, direct labor, shipping, plant overhead and transportation costs. Materials include the cost of corn feedstock, denaturant, and process chemicals. Corn feedstock costs include gains and losses on related derivative financial instruments not designated as cash flow hedges, inbound freight charges, inspection costs and transfer costs, as well as reclassifications of gains and losses on cash flow hedges from accumulated other comprehensive income or loss. Direct labor includes all compensation and related benefits of non-management personnel involved in production. Shipping costs incurred by the company, including railcar costs, are also reflected in cost of goods sold. Plant overhead consists primarily of plant utilities, and repairs and maintenance. Transportation costs include railcar leases, freight and shipping of the company's products, as well as storage costs incurred at destination terminals. The company uses exchange-traded futures and options contracts and forward purchase and sale contracts to attempt to minimize the effect of price changes on ethanol, renewable corn oil, grain and natural gas. Exchange-traded futures and options contracts are valued at quoted market prices and settled predominantly in cash. The company is exposed to loss when counterparties default on forward purchase and sale contracts. Grain inventories held for sale and forward purchase and sale contracts are valued at market prices when available or other market quotes adjusted for basis differences, primarily in transportation, between the exchange-traded market and local market where the terms of the contract are 11 Table of Contents based. Changes in forward purchase contracts and exchange-traded futures and options contracts are recognized as a component of cost of goods sold. Derivative Financial Instruments The company uses various derivative financial instruments, including exchange-traded futures and exchange-traded and over-the-counter options contracts, to attempt to minimize risk and the effect of commodity price changes including but not limited to, corn, ethanol, natural gas and other agricultural and energy products. The company monitors and manages this exposure as part of its overall risk management policy to reduce the adverse effect market volatility may have on its operating results. The company may hedge these commodities as one way to mitigate risk; however, there may be situations when these hedging activities themselves result in losses. By using derivatives to hedge exposures to changes in commodity prices, the company is exposed to credit and market risk. The company’s exposure to credit risk includes the counterparty’s failure to fulfill its performance obligations under the terms of the derivative contract. The company minimizes its credit risk by entering into transactions with high quality counterparties, limiting the amount of financial exposure it has with each counterparty and monitoring their financial condition. Market risk is the risk that the value of the financial instrument might be adversely affected by a change in commodity prices or interest rates. The company manages market risk by incorporating parameters to monitor exposure within its risk management strategy, which limits the types of derivative instruments and strategies the company can use and the degree of market risk it can take using derivative instruments. Forward contracts are recorded at fair value unless the contracts qualify for, and the company elects, normal purchase or sale exceptions. Changes in fair value are recorded in operating income unless the contracts qualify for, and the company elects, cash flow hedge accounting treatment. Certain qualifying derivatives related to ethanol production and agribusiness and energy services are designated as cash flow hedges. The company evaluates the derivative instrument to ascertain its effectiveness prior to entering into cash flow hedges. Unrealized gains and losses are reflected in accumulated other comprehensive income or loss until the gain or loss from the underlying hedged transaction is realized and the physical transaction is completed. When it becomes probable a forecasted transaction will not occur, the cash flow hedge treatment is discontinued, which affects earnings. These derivative financial instruments are recognized in current assets or current liabilities at fair value. At times, the company hedges its exposure to changes in inventory values and designates qualifying derivatives as fair value hedges. The carrying amount of the hedged inventory is adjusted in the current period for changes in fair value. Estimated fair values carried at market are based on exchange-quoted prices, adjusted as appropriate for regional location basis values which represent differences in local markets including transportation as well as quality or grade differences. Basis values are generally determined using inputs from broker quotations or other market transactions. However, a portion of the value may be derived using unobservable inputs. Ineffectiveness of the hedges is recognized in the current period to the extent the change in fair value of the inventory is not offset by the change in fair value of the derivative. Assets Held for Sale In accordance with ASC 360, Property, Plant, Equipment , the company determined the carrying values of certain assets classified as held for sale were not recoverable and exceeded their fair values. The company then measured the impairment losses by comparing the book values with current third-party quoted market prices, resulting in a total impairment of $ 10.7 million, which is recorded within impairment of assets held for sale in the ethanol production segment on the consolidated statements of operations for the nine months ended September 30, 2025. After the impairment, we have $ 5.5 million of assets held for sale as of September 30, 2025, which were recorded in the ethanol production segment within property and equipment, net of accumulated depreciation and amortization on the consolidated balance sheets. Investments in Equity Method Investees On June 30, 2025, the company disposed of its 50 % investment in GP Turnkey Tharaldson, which was accounted for on an equity method basis. Refer to Note 3 - Merger and Dispositions for further analysis. As of December 31, 2024, the 12 Table of Contents company's investment in GP Turnkey Tharaldson totaled $ 51.6 million recorded in other assets on the consolidated balance sheet. Product Financing Arrangement During the second quarter of 2025, the company entered into a product financing arrangement with a financial institution in which it received up front payment for corn oil that the company has an obligation to repurchase in weekly increments through January of 2026. In accordance with ASC 606, Revenue from Contracts with Customers ("ASC 606"), this agreement was accounted for as a financing transaction and revenue is precluded. As of September 30, 2025, a liability of $ 20.9 million was recorded within product financing arrangement on the consolidated balance sheets. Carbon Equipment Liabilities The company has engaged Tallgrass High Plains Carbon Storage, LLC and its affiliates to construct carbon sequestration equipment at its three Nebraska plants in order to maximize tax credit potential related to the production of low carbon fuels. The equipment build is in process as of September 30, 2025, and the company has executed a financing agreement in which the cost of the project will be paid monthly over 12 years commencing once the facilities are in service. The company has recorded total project spend to date within carbon equipment liabilities on the consolidated balance sheets. The facilities are currently estimated to be placed in service in the fourth quarter. Once the facilities are placed in service, the amounts presented as carbon equipment liabilities will be reclassified and presented as debt on the consolidated balance sheets. Income Tax Benefit The company has determined that it qualifies for clean fuel production tax credits allowable under the IRA and OBBB. The credits are recognized as a tax benefit in the period in which production occurs, and the product is sold in a qualifying manner. The tax benefit recognized is determined based on the company's CI score to date and the expected sales price of the credits. The credits are recorded within income tax benefit on the consolidated statements of operations. 13 Table of Contents 2. REVENUE Revenue by Source The following tables disaggregate revenue by major source (in thousands): Three Months Ended September 30, 2025 Ethanol Production Agribusiness & Energy Services Eliminations Total Revenues Revenues from contracts with customers under ASC 606 Ethanol $ — $ — $ — $ — Distillers grains 25,524 5,524 — 31,048 Renewable corn oil — — — — Other 12,979 702 — 13,681 Intersegment revenues 347 71 ( 418 ) — Total revenues from contracts with customers 38,850 6,297 ( 418 ) 44,729 Revenues from contracts accounted for as derivatives under ASC 815 (1) Ethanol 343,451 15,660 — 359,111 Distillers grains 44,313 8,158 — 52,471 Renewable corn oil 47,298 — — 47,298 Other — 4,878 — 4,878 Intersegment revenues — 5,796 ( 5,796 ) — Total revenues from contracts accounted for as derivatives 435,062 34,492 ( 5,796 ) 463,758 Total Revenues $ 473,912 $ 40,789 $ ( 6,214 ) $ 508,487 Nine Months Ended September 30, 2025 Ethanol Production Agribusiness & Energy Services Eliminations Total Revenues Revenues from contracts with customers under ASC 606 Ethanol $ — $ — $ — $ — Distillers grains 68,621 12,029 — 80,650 Renewable corn oil — — — — Other 63,280 2,834 — 66,114 Intersegment revenues 860 200 ( 1,060 ) — Total revenues from contracts with customers 132,761 15,063 ( 1,060 ) 146,764 Revenues from contracts accounted for as derivatives under ASC 815 (1) Ethanol 1,094,711 101,982 — 1,196,693 Distillers grains 155,596 17,471 — 173,067 Renewable corn oil 115,769 — — 115,769 Other — 30,538 — 30,538 Intersegment revenues — 17,095 ( 17,095 ) — Total revenues from contracts accounted for as derivatives 1,366,076 167,086 ( 17,095 ) 1,516,067 Total Revenues $ 1,498,837 $ 182,149 $ ( 18,155 ) $ 1,662,831 14 Table of Contents Three Months Ended September 30, 2024 Ethanol Production Agribusiness & Energy Services Eliminations Total Revenues Revenues from contracts with customers under ASC 606 Ethanol $ — $ — $ — $ — Distillers grains 19,597 4,521 — 24,118 Renewable corn oil — — — — Other 12,919 2,015 — 14,934 Intersegment revenues 1,075 69 ( 1,144 ) — Total revenues from contracts with customers 33,591 6,605 ( 1,144 ) 39,052 Revenues from contracts accounted for as derivatives under ASC 815 (1) Ethanol 439,981 76,014 — 515,995 Distillers grains 53,915 8,618 — 62,533 Renewable corn oil 35,859 3,346 — 39,205 Other 1,293 657 — 1,950 Intersegment revenues — 6,620 ( 6,620 ) — Total revenues from contracts accounted for as derivatives 531,048 95,255 ( 6,620 ) 619,683 Total Revenues $ 564,639 $ 101,860 $ ( 7,764 ) $ 658,735 Nine Months Ended September 30, 2024 Ethanol Production Agribusiness & Energy Services Eliminations Total Revenues Revenues from contracts with customers under ASC 606 Ethanol $ — $ — $ — $ — Distillers grains 67,676 5,039 — 72,715 Renewable corn oil — — — — Other 42,536 6,483 — 49,019 Intersegment revenues 3,467 233 ( 3,700 ) — Total revenues from contracts with customers 113,679 11,755 ( 3,700 ) 121,734 Revenues from contracts accounted for as derivatives under ASC 815 (1) Ethanol 1,177,189 235,512 — 1,412,701 Distillers grains 195,683 23,871 — 219,554 Renewable corn oil 103,424 3,346 — 106,770 Other 5,766 8,249 — 14,015 Intersegment revenues — 19,072 ( 19,072 ) — Total revenues from contracts accounted for as derivatives 1,482,062 290,050 ( 19,072 ) 1,753,040 Total Revenues $ 1,595,741 $ 301,805 $ ( 22,772 ) $ 1,874,774 (1) Revenues from contracts accounted for as derivatives represent physically settled derivative sales that are outside the scope of ASC 606. Major Customers Revenues from Customer A represented 71 % and 37 % of total revenues for the three and nine months ended September 30, 2025, respectively, recorded within the ethanol production segment. For the three and nine months ended September 30, 2024, Customer B represented 13 % of total revenues recorded within the ethanol production segment. 15 Table of Contents 3. MERGER AND DISPOSITIONS Green Plains Obion LLC Disposition On August 27, 2025, Green Plains Inc. announced that its wholly owned subsidiary, Green Plains Obion LLC, entered into an asset purchase agreement for the sale of the ethanol plant located in Rives, Tennessee, to POET Biorefining - Obion, LLC. On September 25, 2025, the company closed on the sale and received proceeds of $ 170 million plus related working capital of $ 13.8 million (the “POET Transaction”). A gain of $ 36.0 million was recorded in gain on sale of assets, net on the consolidated statements of operations. The proceeds from the sale were used to repay the outstanding balance of the junior secured mezzanine notes due 2026 and to supplement corporate liquidity. The company incurred transaction costs of $ 5.2 million related to the POET Transaction during the three and nine months ended September 30, 2025. These costs consisted primarily of financial advisory services, legal services and other professional fees, and were recorded as a reduction of gain on sale of assets, net. The assets sold and liabilities transferred of the POET Transaction at closing on September 25, 2025 were as follows (in thousands): Amounts of Identifiable Assets Disposed and Liabilities Relinquished Inventories $ 19,485 Prepaid expenses and other 21 Derivative financial instruments 14 Property and equipment 127,077 Operating lease right-of-use assets 3,739 Accounts payable ( 5,462 ) Accrued and other liabilities ( 2,243 ) Operating lease current liabilities ( 1,687 ) Operating lease long-term liabilities ( 2,052 ) Debt ( 657 ) Total identifiable net assets disposed $ 138,235 The amounts reflected above represent preliminary amounts subject to post-closing working capital adjustments, which had not been finalized as of September 30, 2025. Proventus LLC Disposition On May 31, 2025, the company completed the sale of its 75 % interest in Proventus LLC for net proceeds of $ 0.4 million. The company recorded a pretax loss on the sale of $ 4.0 million during the nine months ended September 30, 2025 within loss on sale of assets on the consolidated statements of operations. Net assets sold at closing, consisting of property and equipment, totaled $ 9.0 million. As part of the transaction, the company removed $ 4.5 million of non-controlling interest in Proventus LLC, which was included in the calculation of the pretax loss disclosed above. GP Turnkey Tharaldson LLC Disposition On June 30, 2025, the company sold its 50 % investment in GP Turnkey Tharaldson LLC for $ 25.0 million. Proceeds from the disposal are estimated at $ 25.0 million. The balance of the equity method investment on the date of the disposal was $ 51.2 million. A preliminary pretax loss of $ 26.2 million was recorded during the nine months ended September 30, 2025 within loss from equity method investees, net of income taxes on the consolidated statements of operations. Green Plains Partners Merger On January 9, 2024, the transactions contemplated by the Merger Agreement were completed and the company issued approximately 4.7 million shares of common stock to acquire all of the publicly held common units of the partnership not already owned by the company prior to the Merger at a fixed exchange ratio of 0.405 shares of the company's common stock, par value $ 0.001 per share, along with $ 2.50 of cash consideration for each partnership common unit. The total 16 Table of Contents consideration as a result of the Merger was $ 143.1 million, which was comprised of $ 29.2 million in cash and $ 113.9 million of common stock exchanged. As a result of the Merger, the partnership's common units are no longer publicly traded. The interests in the partnership owned by the company and its subsidiaries remain outstanding as limited partner interests in the surviving entity. The General Partner of the partnership will continue to own the non-economic general partner interest in the surviving entity. Since the company controlled the partnership prior to the Merger and continues to control the partnership after the Merger, the company accounted for the change in its ownership interest in the partnership as an equity transaction during the nine months ended September 30, 2024, which is reflected as a reduction of non-controlling interest with a corresponding increase to common stock and additional paid-in capital. No gain or loss was recognized in the consolidated statements of operations as a result of the Merger. Prior to the effective time of the Merger on January 9, 2024, public unitholders owned a 49.2 % limited partner interest, the company owned a 48.8 % limited partner interest and a 2.0 % general partner interest in the partnership. For the nine months ended September 30, 2024, the non-controlling interest attributed to the partnership common units held by the public of $ 133.8 million were recorded as a reduction of non-controlling interest with a corresponding increase to additional paid-in capital. The company incurred transaction costs of $ 5.5 million related to the Merger during the nine months ended September 30, 2024. These costs were directly related to the Merger consisting primarily of financial advisory services, legal services and other professional fees, and were recorded as an offset to the issuance of common stock within additional paid-in capital. Disposition of Birmingham Terminal On September 30, 2024, the company completed the sale of the terminal located in Birmingham, Alabama and certain related assets and transfer of liabilities (the "Birmingham Transaction") for a sale price of $ 47.5 million, plus working capital of $ 1.2 million. The company recorded a pretax gain on the sale of $ 30.7 million. The proceeds from the sale were used to repay the outstanding balance of the Green Plains Partners term loan due July 20, 2026. The assets sold and liabilities transferred of the Birmingham Transaction at closing on September 30, 2024 were as follows (in thousands): Amounts of Identifiable Assets Disposed and Liabilities Relinquished Prepaid expenses and other $ 1,209 Property and equipment 7,012 Operating lease right-of-use assets 2,208 Goodwill 10,598 Operating lease current liabilities ( 427 ) Operating lease long-term liabilities ( 2,312 ) Other liabilities ( 556 ) Total identifiable net assets disposed $ 17,732 4. FAIR VALUE DISCLOSURES The following methods, assumptions and valuation techniques were used in estimating the fair value of the company’s financial instruments: Level 1 – unadjusted quoted prices in active markets for identical assets or liabilities the company can access at the measurement date. Level 2 – directly or indirectly observable inputs such as quoted prices for similar assets or liabilities in active markets other than quoted prices included within Level 1, quoted prices for identical or similar assets in markets that are not active, and other inputs that are observable or can be substantially corroborated by observable market data through correlation or 17 Table of Contents other means. Fair value hedged inventories in the agribusiness and energy services segment as well as forward commodity purchase and sale contracts are valued at nearby futures values, plus or minus nearby basis values, which represent differences in local markets, including transportation or commodity quality or grade differences. Level 3 – unobservable inputs that are supported by little or no market activity and comprise a significant component of the fair value of the assets or liabilities. Derivative contracts include exchange-traded commodity futures and options contracts and forward commodity purchase and sale contracts. Exchange-traded futures and options contracts are valued based on unadjusted quoted prices in active markets and are classified in Level 1. The majority of the company’s exchange-traded futures and options contracts are cash-settled on a daily basis. There have been no changes in valuation techniques and inputs used in measuring fair value. The company’s assets and liabilities by level are as follows (in thousands): Fair Value Measurements at September 30, 2025 Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Unobservable Inputs (Level 3) Total Assets Cash and cash equivalents $ 135,903 $ — $ — $ 135,903 Restricted cash 75,722 — — 75,722 Inventories carried at market — 14,241 — 14,241 Derivative financial instruments - assets — 6,126 — 6,126 Property and equipment, net of accumulated depreciation and amortization (1) — — 5,500 5,500 Total assets measured at fair value $ 211,625 $ 20,367 $ 5,500 $ 237,492 Liabilities Accounts payable (2) $ — $ 14,792 $ — $ 14,792 Accrued and other liabilities (3) — 4,667 — 4,667 Derivative financial instruments - liabilities — 6,497 — 6,497 Other liabilities (3) — 35 — 35 Total liabilities measured at fair value $ — $ 25,991 $ — $ 25,991 18 Table of Contents Fair Value Measurements at December 31, 2024 Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Unobservable Inputs (Level 3) Total Assets Cash and cash equivalents $ 173,041 $ — $ — $ 173,041 Restricted cash 36,354 — — 36,354 Inventories carried at market — 48,500 — 48,500 Derivative financial instruments - assets — 10,154 — 10,154 Total assets measured at fair value $ 209,395 $ 58,654 $ — $ 268,049 Liabilities Accounts payable (2) $ — $ 23,208 $ — $ 23,208 Accrued and other liabilities (3) — 2,094 — 2,094 Derivative financial instruments - liabilities — 4,791 — 4,791 Other liabilities (3) — 979 — 979 Total liabilities measured at fair value $ — $ 31,072 $ — $ 31,072 (1) Property and equipment, net of accumulated depreciation and amortization includes $ 5.5 million of assets held for sale at September 30, 2025. (2) Accounts payable is generally stated at historical amounts with the exception of $ 14.8 million and $ 23.2 million at September 30, 2025 and December 31, 2024, respectively, related to certain delivered inventory for which the payable fluctuates based on changes in commodity prices. These payables are hybrid financial instruments for which the company has elected the fair value option. (3) Accrued and other liabilities includes $ 4.7 million and $ 2.1 million at September 30, 2025 and December 31, 2024, respectively, while other liabilities includes $ 1.0 million of consideration related to potential earn-out payments recorded at fair value at December 31, 2024. As of September 30, 2025, the fair value of the company’s debt was approximately $ 331.7 million compared with a book value of $ 353.4 million. At December 31, 2024, the fair value of the company’s debt was approximately $ 518.6 million compared with a book value of $ 575.4 million. The company estimated the fair value of its outstanding debt using Level 2 inputs. The company believes the fair value of its accounts receivable approximated book value, which was $ 84.9 million and $ 94.9 million at September 30, 2025 and December 31, 2024, respectively. The fair values of tangible assets and goodwill acquired represent Level 3 measurements which were derived using a combination of the income approach, market approach and cost approach for the specific assets or liabilities being valued. 5. SEGMENT INFORMATION The company reports the financial and operating performance for the following two operating segments: (1) ethanol production, which includes the production, storage and transportation of ethanol, distillers grains, Ultra-High Protein and renewable corn oil and (2) agribusiness and energy services, which includes grain handling and storage, commodity marketing and merchant trading for company-produced and third-party ethanol, distillers grains, Ultra-High Protein, renewable corn oil, natural gas and other commodities. Corporate activities include selling, general and administrative expenses, consisting primarily of compensation, professional fees, overhead costs, gain on sale of assets, net, and restructuring costs not directly related to a specific operating segment. During the normal course of business, the operating segments conduct business with each other. For example, the agribusiness and energy services segment procures grain and natural gas and sells products, including ethanol, distillers grains, Ultra-High Protein and renewable corn oil for the ethanol production segment. These intersegment activities are treated like third-party transactions with origination, marketing and storage fees charged at estimated market values. Consequently, these transactions affect segment performance; however, they do not impact the company’s consolidated results since the revenues and corresponding costs are eliminated. 19 Table of Contents The Chief Operating Decision Maker ("CODM") for the company is the Chief Executive Officer. The CODM utilizes EBITDA to assess segment performance, which is derived from revenue less cost of goods sold and selling, general and administrative expenses. The CODM manages and allocates resources to the operations of the company's two segments. This enables the CODM to assess the company’s overall level of available resources and determine how best to deploy these resources for capital expenditure, research and development projects, and other strategic opportunities that are in line with our long-term strategic goals. The CODM is regularly provided with consolidated expense information or forecasted expense information for the applicable reportable segment. The following tables set forth certain financial data for the company’s operating segments (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Revenues Ethanol production Revenues from external customers $ 473,565 $ 563,564 $ 1,497,977 $ 1,592,274 Intersegment revenues 347 1,075 860 3,467 Total segment revenues 473,912 564,639 1,498,837 1,595,741 Agribusiness and energy services Revenues from external customers 34,922 95,171 164,854 282,500 Intersegment revenues 5,867 6,689 17,295 19,305 Total segment revenues 40,789 101,860 182,149 301,805 Revenues including intersegment activity 514,701 666,499 1,680,986 1,897,546 Intersegment eliminations ( 6,214 ) ( 7,764 ) ( 18,155 ) ( 22,772 ) $ 508,487 $ 658,735 $ 1,662,831 $ 1,874,774 Refer to Note 2 - Revenue , for further disaggregation of revenue by operating segment. Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Cost of goods sold Ethanol production (1) $ 431,367 $ 498,326 $ 1,428,494 $ 1,501,681 Agribusiness and energy services 31,168 90,064 155,717 271,566 Intersegment eliminations ( 6,214 ) ( 7,764 ) ( 18,155 ) ( 22,772 ) $ 456,321 $ 580,626 $ 1,566,056 $ 1,750,475 Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Gross margin Ethanol production (1) (2) $ 42,545 $ 66,313 $ 70,343 $ 94,060 Agribusiness and energy services 9,621 11,796 26,432 30,239 $ 52,166 $ 78,109 $ 96,775 $ 124,299 20 Table of Contents Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Depreciation and amortization Ethanol production $ 23,868 $ 21,444 $ 67,821 $ 62,522 Agribusiness and energy services (3) 252 505 4,710 1,507 Corporate activities (4) 848 4,121 2,384 5,112 $ 24,968 $ 26,070 $ 74,915 $ 69,141 Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Operating income (loss) Ethanol production (1) (2) (5) $ 4,374 $ 35,240 $ ( 47,394 ) $ ( 626 ) Agribusiness and energy services (3) 6,942 7,830 10,224 16,000 Corporate activities (4) (6) (7) 22,553 12,982 ( 19,584 ) ( 21,922 ) $ 33,869 $ 56,052 $ ( 56,754 ) $ ( 6,548 ) (1) Ethanol production includes inventory lower of cost or net realizable value adjustments of $ 0.3 million and $ 10.1 million for the three and nine months ended September 30, 2025 and 2024, respectively. (2) Ethanol production includes margins from a one-time sale of accumulated RINs of $ 22.6 million for the nine months ended September 30, 2025. (3) Depreciation and amortization for agribusiness and energy services includes impairment of property and equipment of $ 3.1 million for the nine months ended September 30, 2025. (4) Depreciation and amortization for corporate activities includes impairment of a research and development technology intangible asset of $ 3.5 million for the three and nine months ended September 30, 2024. (5) Ethanol production includes impairment of assets held for sale of $ 10.7 million for the nine months ended September 30, 2025. (6) Corporate activities includes $ 1.5 million and $ 13.5 million of restructuring costs for the three and nine months ended September 30, 2025, respectively, as a result of the company's cost reduction initiative, including severance related to the departure of its former CEO. (7) Corporate activities include a pretax gain on sale of assets, net of $ 36.0 million and $ 32.0 million for the three and nine months ended September 30, 2025, respectively, and $ 30.7 million for the three and nine months ended September 30, 2024. During the three and nine months ended September 30, 2025, the company incurred restructuring costs related to severance, stock based compensation and other charges as a result of cost reduction initiatives that were recorded within the following line items in the consolidated statements of operations (in thousands): Three Months Ended September 30, 2025 Ethanol production Agribusiness and energy services Corporate activities Subtotal Cost of goods sold $ 28 $ 113 $ — $ 141 Selling, general and administrative expenses 6 13 1,539 1,558 Other, net 223 787 — 1,010 Total restructuring costs $ 257 913 1,539 $ 2,709 21 Table of Contents Nine Months Ended September 30, 2025 Ethanol production Agribusiness and energy services Corporate activities Subtotal Cost of goods sold $ 2,373 $ 710 $ — $ 3,083 Selling, general and administrative expenses 480 2,050 13,533 16,063 Other, net 223 941 1,505 2,669 Total restructuring costs $ 3,076 3,701 15,038 $ 21,815 The following tables reconcile EBITDA, our segment measure of profit or loss, to net income (loss) (in thousands). EBITDA is defined as earnings before interest expense, income taxes, depreciation and amortization excluding the amortization of right-of-use assets and debt issuance costs. Three Months Ended September 30, 2025 Ethanol production Agribusiness and energy services Subtotal EBITDA $ 28,664 $ 6,665 $ 35,329 Depreciation and amortization ( 23,868 ) ( 252 ) ( 24,120 ) Interest expense ( 42,575 ) ( 1,126 ) ( 43,701 ) Subtotal $ ( 37,779 ) $ 5,287 $ ( 32,492 ) Unallocated corporate expenses (1) 17,835 Income tax benefit, net of equity method income tax expense 25,631 Net income (loss) $ 10,974 Nine Months Ended September 30, 2025 Ethanol production Agribusiness and energy services Subtotal EBITDA $ 18,240 $ 14,849 $ 33,089 Depreciation and amortization ( 67,821 ) ( 4,710 ) ( 72,531 ) Interest expense ( 54,005 ) ( 5,480 ) ( 59,485 ) Subtotal $ ( 103,586 ) $ 4,659 $ ( 98,927 ) Unallocated corporate expenses (1) ( 58,878 ) Income tax benefit, inclusive of equity method income tax benefit 23,911 Net income (loss) $ ( 133,894 ) 22 Table of Contents Three Months Ended September 30, 2024 Ethanol production Agribusiness and energy services Subtotal EBITDA $ 56,144 $ 8,754 $ 64,898 Depreciation and amortization ( 21,444 ) ( 505 ) ( 21,949 ) Interest expense ( 7,051 ) ( 1,470 ) ( 8,521 ) Subtotal $ 27,649 $ 6,779 $ 34,428 Unallocated corporate expenses (1) 12,731 Income tax expense, net of equity method income tax benefit 1,478 Net income (loss) $ 48,637 Nine Months Ended September 30, 2024 Ethanol production Agribusiness and energy services Subtotal EBITDA $ 60,475 $ 18,855 $ 79,330 Depreciation and amortization ( 62,522 ) ( 1,507 ) ( 64,029 ) Interest expense ( 16,974 ) ( 3,632 ) ( 20,606 ) Subtotal $ ( 19,021 ) $ 13,716 $ ( 5,305 ) Unallocated corporate expenses (1) ( 22,640 ) Income tax expense, net of equity method income tax benefit 1,422 Net income (loss) $ ( 26,523 ) (1) Corporate expenses include selling, general administrative expenses, depreciation and amortization, gain on sale of assets, net, interest expense, and during 2025 includes restructuring costs related to cost savings initiatives and the departure of our former CEO as well as losses on sale of equity method investment. The following table sets forth total assets by operating segment (in thousands): September 30, 2025 December 31, 2024 Total assets (1) Ethanol production $ 1,107,365 $ 1,234,635 Agribusiness and energy services 257,644 412,006 Corporate assets 172,201 143,716 Intersegment eliminations ( 4,727 ) ( 8,183 ) $ 1,532,483 $ 1,782,174 (1) Asset balances by segment exclude intercompany balances. 6. INVENTORIES Inventories are carried at the lower of cost or net realizable value, except fair-value hedged inventories. There was a $ 0.3 million and $ 2.1 million lower of cost or net realizable value inventory adjustment associated with finished goods in cost of goods sold within the ethanol production segment as of September 30, 2025 and December 31, 2024, respectively. 23 Table of Contents The components of inventories are as follows (in thousands): September 30, 2025 December 31, 2024 Finished goods $ 26,908 $ 72,863 Commodities held for sale 14,241 48,500 Raw materials 11,893 37,334 Work-in-process 10,585 13,569 Supplies and parts 63,341 55,178 $ 126,968 $ 227,444 7. DERIVATIVE FINANCIAL INSTRUMENTS At September 30, 2025, the company’s consolidated balance sheet reflected unrealized losses of $ 13.0 million, net of tax, in accumulated other comprehensive loss. The company expects these items will be reclassified as operating loss over the next 12 months as a result of hedged transactions that are forecasted to occur. The amount realized in operating loss will differ as commodity prices change. Fair Values of Derivative Instruments The fair values of the company’s derivative financial instruments and the line items on the consolidated balance sheets where they are reported are as follows (in thousands): Asset Derivatives' Fair Value Liability Derivatives' Fair Value September 30, 2025 December 31, 2024 September 30, 2025 December 31, 2024 Derivative financial instruments - forwards $ 6,126 (1) $ 10,154 $ 6,497 (2) $ 4,791 (3) Other liabilities — — 35 15 Total $ 6,126 $ 10,154 $ 6,532 $ 4,806 (1) At September 30, 2025, derivative financial instruments, as reflected on the balance sheet, includes net unrealized gains on exchange-traded futures and options contracts of $ 0.9 million and the balance representing economic hedges. (2) At September 30, 2025, derivative financial instruments, as reflected on the balance sheet, includes net unrealized losses on exchange-traded futures and options contracts of $ 21.2 million, which included $ 16.6 million of net unrealized losses on derivative financial instruments designated as cash flow hedging instruments, $ 1.2 million of unrealized gains on derivative financial instruments designated as fair value hedging instruments, and the balance representing economic hedges. (3) At December 31, 2024, derivative financial instruments, as reflected on the balance sheet, includes net unrealized losses on exchange-traded futures and options contracts of $ 4.7 million, which include $ 0.5 million of net unrealized gains on derivative financial instruments designated as cash flow hedging instruments, $ 3.0 million of unrealized losses on derivative financial instruments designated as fair value hedging instruments, and the balance representing economic hedges. Refer to Note 4 - Fair Value Disclosures , which contains fair value information related to derivative financial instruments. 24 Table of Contents Effect of Derivative Instruments on Consolidated Balance Sheets, Consolidated Statements of Operations and Consolidated Statements of Comprehensive Income (Loss) The gains or losses recognized in income and other comprehensive income related to the company’s derivative financial instruments and the line items on the consolidated financial statements where they are reported are as follows (in thousands): Amount of Gain (Loss) Reclassified from Accumulated Other Comprehensive Income into Income Location of Gain (Loss) Reclassified from Accumulated Other Comprehensive Income into Income Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Revenues $ ( 1,169 ) $ 5,146 $ ( 1,194 ) $ 8,882 Cost of goods sold ( 6,627 ) ( 13,088 ) ( 10,325 ) ( 26,109 ) Income (loss) recognized in income (loss) before income taxes $ ( 7,796 ) $ ( 7,942 ) $ ( 11,519 ) $ ( 17,227 ) Amount of Gain (Loss) Recognized in Other Comprehensive Income on Derivatives Gain (Loss) Recognized in Other Comprehensive Income on Derivatives Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Commodity contracts $ ( 16,185 ) $ 459 $ ( 30,222 ) $ ( 8,363 ) A portion of the company’s derivative instruments are considered economic hedges and as such are not designated as hedging instruments. The company uses exchange-traded futures and options contracts to manage its net position of product inventories and forward cash purchase and sales contracts to reduce price risk caused by market fluctuations. Derivatives, including exchange traded contracts and forward commodity purchase or sale contracts, and inventories of certain agricultural products, which include amounts acquired under deferred pricing contracts, are stated at fair value. Fair value estimates are based on exchange-quoted prices, adjusted as appropriate for regional location basis value, which represent differences in local markets including transportation as well as quality or grade differences. Amount of Gain (Loss) Recognized in Income on Derivatives Derivatives Not Designated as Hedging Instruments Location of Gain (Loss) Recognized in Income on Derivatives Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Exchange-traded futures and options Revenues $ ( 10,981 ) $ 10,253 $ ( 5,662 ) $ 9,034 Forwards Revenues ( 2,334 ) 708 ( 926 ) ( 3,736 ) Exchange-traded futures and options Cost of goods sold 915 4,555 3,399 16,209 Forwards Cost of goods sold 4,090 6,781 ( 3,762 ) 90 Net gain (loss) recognized in income (loss) before income taxes $ ( 8,310 ) $ 22,297 $ ( 6,951 ) $ 21,597 25 Table of Contents The following amounts were recorded on the consolidated balance sheets related to cumulative basis adjustments for the fair value hedged items (in thousands): September 30, 2025 December 31, 2024 Line Item in the Consolidated Balance Sheet in Which the Hedged Item is Included Carrying Amount of the Hedged Assets Cumulative Amount of Fair Value Hedging Adjustment Included in the Carrying Amount of the Hedged Assets Carrying Amount of the Hedged Assets Cumulative Amount of Fair Value Hedging Adjustment Included in the Carrying Amount of the Hedged Assets Inventories $ 14,241 $ ( 618 ) $ 48,500 $ 8,166 Effect of Cash Flow and Fair Value Hedge Accounting on the Statements of Operations Location and Amount of Gain (Loss) Recognized in Income on Cash Flow and Fair Value Hedging Relationships for the Three Months Ended September 30, 2025 2024 Revenue Cost of Goods Sold Revenue Cost of Goods Sold Gain (loss) on cash flow hedging relationships Commodity contracts Amount of gain (loss) on exchange-traded futures reclassified from accumulated other comprehensive income into income $ ( 1,169 ) $ ( 6,627 ) $ 5,146 $ ( 13,088 ) Gain (loss) on fair value hedging relationships Commodity contracts Fair-value hedged inventories — 52 — 3,611 Exchange-traded futures designated as hedging instruments — 800 — ( 2,485 ) Total amounts of income and expense line items presented in the statement of operations in which the effects of cash flow or fair value hedges are recorded $ ( 1,169 ) $ ( 5,775 ) $ 5,146 $ ( 11,962 ) 26 Table of Contents Location and Amount of Gain (Loss) Recognized in Income on Cash Flow and Fair Value Hedging Relationships for the Nine Months Ended September 30, 2025 2024 Revenue Cost of Goods Sold Revenue Cost of Goods Sold Gain (loss) on cash flow hedging relationships Commodity contracts Amount of gain (loss) on exchange traded futures reclassified from accumulated other comprehensive income into income $ ( 1,194 ) $ ( 10,325 ) $ 8,882 $ ( 26,109 ) Gain (loss) on fair value hedging relationships Commodity contracts Fair-value hedged inventories — ( 59 ) — 264 Exchange-traded futures designated as hedging instruments — 2,774 — ( 81 ) Total amounts of income and expense line items presented in the statement of operations in which the effects of cash flow or fair value hedges are recorded $ ( 1,194 ) $ ( 7,610 ) $ 8,882 $ ( 25,926 ) The notional volume of open commodity derivative positions as of September 30, 2025 are as follows (in thousands): Exchange-Traded (1) Non-Exchange-Traded (2) Derivative Instruments Net Long & (Short) Long (Short) Unit of Measure Commodity Futures ( 8,450 ) Bushels Corn Futures 58,545 (3) Bushels Corn Futures ( 33,810 ) Gallons Ethanol Futures ( 173,922 ) (3) Gallons Ethanol Futures ( 2,280 ) MmBTU Natural Gas Futures 5,378 (3) MmBTU Natural Gas Futures ( 4,755 ) (4) MmBTU Natural Gas Futures ( 26,640 ) Pounds Soybean Oil Futures ( 1,000 ) Bushels Soybeans Options 3,931 Gallons Ethanol Options 1,034 Bushels Soybeans Options 200 MmBTU Natural Gas Forwards 25,209 — Bushels Corn Forwards 12,797 ( 171,280 ) Gallons Ethanol Forwards 84 ( 242 ) Tons Distillers Grains Forwards — ( 50,671 ) Pounds Renewable Corn Oil Forwards 2,783 ( 1,203 ) MmBTU Natural Gas (1) Notional volume of exchange-traded futures and options are presented on a net long and (short) position basis. Options are presented on a delta-adjusted basis. (2) Notional volume of non-exchange-traded forward physical contracts are presented on a gross long and (short) position basis, including both fixed-price and basis contracts, for which only the basis portion of the contract price is fixed. (3) Notional volume of exchange-traded futures used for cash flow hedges. (4) Notional volume of exchange-traded futures used for fair value hedges. 27 Table of Contents Energy trading contracts that do not involve physical delivery are presented net in revenues on the consolidated statements of operations. Included in revenues are net gains of $ 3.4 million and net gains of $ 8.7 million for the three and nine months ended September 30, 2025, respectively, and net gains of $ 1.0 million and $ 3.3 million for the three and nine months ended September 30, 2024, respectively, on energy trading contracts. 8. DEBT The components of long-term debt are as follows (in thousands): September 30, 2025 December 31, 2024 Corporate 2.25 % convertible notes due 2027 (1) $ 230,000 $ 230,000 Green Plains SPE LLC Junior secured mezzanine notes due 2026 (2) — 125,000 Green Plains Shenandoah Term loan due 2035 (3) 70,500 71,625 Other 9,931 11,163 Total book value of long-term debt 310,431 437,788 Unamortized debt issuance costs ( 2,017 ) ( 3,210 ) Less: current maturities of long-term debt ( 2,042 ) ( 2,118 ) Total long-term debt $ 306,372 $ 432,460 (1) The 2.25 % notes had $ 1.8 million and $ 2.7 million of unamortized debt issuance costs as of September 30, 2025 and December 31, 2024, respectively. (2) The junior notes had $ 0.2 million of unamortized debt issuance costs as of December 31, 2024. (3) The loan had $ 0.2 million and $ 0.3 million of unamortized debt issuance costs as of September 30, 2025 and December 31, 2024, respectively. The components of short-term notes payable and other borrowings are as follows (in thousands): September 30, 2025 December 31, 2024 Green Plains Finance Company, Green Plains Grain and Green Plains Trade $ 350.0 million revolver $ 25,000 $ 133,500 Green Plains Commodity Management $ 20.0 million hedge line 20,000 7,329 $ 45,000 $ 140,829 Corporate Activities In March 2021, the company issued an aggregate $ 230.0 million of 2.25 % convertible senior notes due on March 15, 2027. The 2.25 % notes bear interest at a rate of 2.25 % per year, payable on March 15 and September 15 of each year. The 2.25 % notes are senior, unsecured obligations of the company. The 2.25 % notes are convertible, at the option of the holders, into consideration consisting of, at the company’s election, cash, shares of the company’s common stock, or a combination of cash and stock (and cash in lieu of fractional shares). However, before September 15, 2026, the 2.25 % notes will not be convertible unless certain conditions are satisfied. The initial conversion rate is 31.6206 shares of the company’s common stock per $1,000 principal amount of 2.25 % notes (equivalent to an initial conversion price of approximately $ 31.62 per share of the company’s common stock), representing an approximately 37.5 % premium over the offering price of the company’s common stock. The conversion rate is subject to adjustment upon the occurrence of certain events, including but not limited to; the event of a stock dividend or stock split; the issuance of additional rights, options and warrants; spinoffs; or a tender or exchange offering. In addition, the company may be obligated to increase the conversion rate for any conversion that occurs in connection with certain corporate events, including the company’s calling the 2.25 % notes for redemption. 28 Table of Contents On and after March 15, 2024, and prior to the maturity date, the company may redeem, for cash, all, but not less than all, of the 2.25 % notes if the last reported sale price of the company’s common stock equals or exceeds 140 % of the applicable conversion price on (i) at least 20 trading days during a 30 consecutive trading day period ending on the trading day immediately prior to the date the company delivers notice of the redemption; and (ii) the trading day immediately before the date of the redemption notice. The redemption price will equal 100 % of the principal amount of the 2.25 % notes to be redeemed, plus any accrued and unpaid interest to, but excluding, the redemption date. In addition, upon the occurrence of a “fundamental change” (as defined in the indenture for the 2.25 % notes), holders of the 2.25 % notes will have the right, at their option, to require the company to repurchase their 2.25 % notes for cash at a price equal to 100 % of the principal amount of the 2.25 % notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. On May 7, 2025, the company entered into a secured $ 30 million revolving credit facility with Ancora Alternatives LLC, that matured on July 30, 2025. The facility bore interest at 10 % on borrowings and had a 0.5 % fee on the unused balance. Interest and fees were due on the 5th of each month. There was no outstanding balance on the facility as of September 30, 2025. In conjunction with this facility, the company issued 1,504,140 warrants to purchase shares of its common stock at an exercise price of $ 0.01 per share. The fair value of these warrants was initially recorded as debt issuance costs and has been fully amortized and recorded within interest expense during the nine months ended September 30, 2025. Ethanol Production Segment On February 9, 2021, Green Plains SPE LLC, a wholly-owned special purpose subsidiary and parent of Green Plains Obion and Green Plains Mount Vernon, issued $ 125.0 million of junior secured mezzanine notes due 2026 (the “Junior Notes”) with BlackRock, a holder of a portion of the company’s common stock. The proceeds of the Junior Notes were used to construct high protein processing systems at the Green Plains Obion and Green Plains Mount Vernon facilities. The Junior Notes were amended on May 7, 2025, which extended the maturity date from February 9, 2026 to May 15, 2026. A $ 2.5 million amendment fee was added to the balance of the Junior Notes, increasing the amount outstanding to $ 127.5 million. The Junior Notes were secured by a pledge of the membership interests in and the real property owned by Green Plains Obion and Green Plains Mount Vernon. Further, warrants previously issued in conjunction with the Junior Notes were revised on May 7, 2025, and $ 7.5 million, the fair value of the revised warrants, was recorded as debt issuance costs. These costs were to be amortized through May 2026. As of July 31, 2025, the Junior Notes were also secured by a pledge of the membership interests in, the assets and the real property owned by Green Plains Madison LLC, Green Plains Superior LLC, Green Plains Fairmont LLC, Green Plains Otter Tail LLC, Green Plains Wood River and Green Plains York LLC, as well as the assets and membership interests of Fluid Quip Mechanical, LLC. The Junior Notes accrued interest at an annual rate of 11.75 % through August 9, 2025. On August 10, 2025, the Junior Notes were amended to extend the maturity date to September 15, 2026, with an amendment fee of 2.5 %, or $ 3.2 million , added to the principal balance of the Junior Notes, payable at the maturity date. The interest rate was increased by 0.5 % after the amendment, and subject to an additional 0.5 % each quarter on each scheduled interest payment date. In addition to previous assets and equity securities pledged, the Junior Notes were then also secured by the assets and the real property owned by Green Plains Central City LLC. The amendment added certain financial covenant requirements, including restrictions on additional debt and certain transfer of assets. Also as part of the amendment, the company executed a subscription agreement with certain funds and accounts under management by BlackRock pursuant to which the company agreed to issue, and certain funds and accounts under management by BlackRock purchased, 3,250,000 stock warrants at a strike price of $ 0.01 per share with a ten year exercise period. The amendment also included the right for such funds and accounts to exchange up to 750,000 warrants for a pro rata share of $ 6 million of outstanding principal of Junior Notes. The subscription agreement obligated the company to register for resale the shares of common stock underlying warrants issued to BlackRock. The entire outstanding principal balance, plus any accrued and unpaid interest was due upon maturity. Green Plains SPE LLC was required to comply with certain financial covenants regarding minimum liquidity at Green Plains and a maximum aggregate loan to value. The Junior Notes could have been retired or refinanced after 42 months with no prepayment premium. The Junior Notes had an unsecured parent guarantee from the company and had certain limitations on distributions, dividends or loans to the company unless there will not exist any event of default. The amendment to the Junior Notes was determined to be a substantial change under ASC 470, Debt , and triggered debt extinguishment treatment. In total, a loss on debt extinguishment of $ 35.7 million was recorded within interest expense during the three and nine months ended September 30, 2025. The loss includes the write-off of unamortized debt issuance costs at the retirement date of the Junior Notes, the fair value of the 3,250,000 million warrants issued on August 10, 2025 and the 2.5 % amendment fee. On September 25, 2025, proceeds from the POET Transaction were used to fully retire the Junior Notes. 29 Table of Contents On September 3, 2020, Green Plains Wood River and Green Plains Shenandoah, wholly-owned subsidiaries of the company, entered into a $ 75.0 million loan agreement with MetLife Real Estate Lending LLC. The loan matures on September 1, 2035 and is secured by substantially all of the assets of the Shenandoah facility, including the MSC™ and CST™ assets installed at that facility. During the second quarter of 2024, the agreement was modified to remove the Wood River facility from the assets considered to be secured under the loan agreement and Green Plains Wood River was removed as a counterparty to the loan agreement. The proceeds from the loan were used to add MSC™ technology at the Wood River and Shenandoah facilities as well as other capital expenditures. The loan bears interest at a fixed rate of 5.02 %, plus an interest rate premium subject to quarterly adjustments from 0.00 % to 1.50 % based on the leverage ratio of total funded debt to EBITDA of Shenandoah. Principal payments of $ 1.5 million per year began in October 2022. Prepayments were prohibited until September 2024. Financial covenants of the loan agreement include a minimum loan to value ratio of 50 %, a minimum fixed charge coverage ratio of 1.25 x, a total debt service reserve of six months of future principal and interest payments and a minimum working capital requirement at Green Plains of not less than $ 0.10 per gallon of nameplate capacity or $ 90.3 million. The loan is guaranteed by the company and has certain limitations on distributions, dividends or loans to Green Plains by Shenandoah unless immediately after giving effect to such action, there will not exist any event of default. At September 30, 2025, the interest rate on the loan was 6.52 %. The company also has small equipment financing loans, finance leases on equipment or facilities, and other forms of debt financing. Agribusiness and Energy Services Segment On March 25, 2022, Green Plains Finance Company, Green Plains Grain and Green Plains Trade (collectively, the “Borrowers”), all wholly owned subsidiaries of the company, together with the company, as guarantor, entered into a five-year , $ 350.0 million senior secured sustainability-linked revolving Loan and Security Agreement (the “Facility”) with a group of financial institutions. This transaction refinanced the separate credit facilities previously held by Green Plains Grain and Green Plains Trade. The Facility matures on March 25, 2027. The Facility includes revolving commitments totaling $ 350.0 million and an accordion feature whereby amounts available under the Facility may be increased by up to $ 100.0 million of new lender commitments subject to certain conditions. Each SOFR rate loan shall bear interest for each day at a rate per annum equal to the Term SOFR rate for the outstanding period plus a Term SOFR adjustment and an applicable margin of 2.25 % to 2.50 %, which is dependent on undrawn availability under the Facility. Each base rate loan shall bear interest at a rate per annum equal to the base rate plus the applicable margin of 1.25 % to 1.50 %, which is dependent on undrawn availability under the Facility. The unused portion of the Facility is also subject to a commitment fee of 0.275 % to 0.375 %, dependent on undrawn availability. Additionally, the applicable margin and commitment fee are subject to certain increases or decreases of up to 0.10 % and 0.025 %, respectively, tied to the company’s achievement of certain sustainability criteria, including the reduction of GHG emissions, recordable incident rate reduction, increased renewable corn oil production and the implementation of technology to produce sustainable ingredients. The Facility contains customary affirmative and negative covenants, as well as the following financial covenants to be calculated as of the last day of any month: the current ratio of the Borrowers shall not be less than 1.00 to 1.00; the collateral coverage ratio of the Borrowers shall not be less than 1.20 to 1.00; and the debt to capitalization ratio of the company shall not be greater than 0.60 to 1.00. The Facility also includes customary events of default, including without limitation, failure to make required payments of principal or interest, material incorrect representations and warranties, breach of covenants, events of bankruptcy and other certain matters. The Facility is secured by the working capital assets of the Borrowers and is guaranteed by the company. At September 30, 2025, the interest rate on the Facility was 7.16 %. Green Plains Commodity Management has an uncommitted secured revolving credit facility to finance margins related to its hedging programs, which is secured by cash and securities held in its brokerage accounts. On June 18, 2025, the credit facility was amended, reducing the $ 40.0 million borrowing limit to $ 20.0 million. During the first quarter of 2023, this revolving credit facility was extended five years to mature on April 30, 2028. Advances are subject to variable interest rates equal to SOFR plus 1.75 %. At September 30, 2025, the interest rate on the facility was 5.88 %. Green Plains Grain has a short-term inventory financing agreement with a financial institution. The company has accounted for the agreement as short-term notes, rather than revenues, and has elected the fair value option to offset 30 Table of Contents fluctuations in market prices of the inventory. This agreement is subject to negotiated variable interest rates. The company had no outstanding short-term notes payable related to the inventory financing agreement as of September 30, 2025. Covenant Compliance The company was in compliance with its debt covenants as of September 30, 2025. Restricted Net Assets At September 30, 2025, there were approximately $ 48.9 million of net assets at the company’s subsidiaries that could not be transferred to the parent company in the form of dividends, loans or advances due to restrictions contained in the credit facilities of these subsidiaries. 9. STOCK-BASED COMPENSATION The company has an equity incentive plan which reserved a total of 6.9 million shares of common stock for issuance pursuant to the plan, of which 1.2 million shares remain available for issuance. The plan provides for shares, including options to purchase shares of common stock, stock appreciation rights tied to the value of common stock, restricted stock, performance share awards, and restricted and deferred stock unit awards, to be granted to eligible employees, non-employee directors and consultants. The company measures stock-based compensation at fair value on the grant date, with no adjustments for estimated forfeitures. The company records noncash compensation expense related to equity awards in its consolidated financial statements over the requisite period on a straight-line basis. Restricted Stock Awards and Deferred Stock Units The restricted non-vested stock awards and deferred stock units activity for the nine months ended September 30, 2025 is as follows: Non-Vested Shares and Deferred Stock Units Weighted- Average Grant- Date Fair Value Weighted-Average Remaining Vesting Term (in years) Non-Vested at December 31, 2024 735,513 $ 23.45 Granted 1,115,387 5.63 Forfeited ( 151,788 ) 16.07 Vested ( 509,260 ) 21.92 Non-Vested at September 30, 2025 1,189,852 $ 8.34 1.9 Performance Share Awards On March 10, 2025, March 13, 2024, and March 9, 2023, the Compensation Committee of the Board granted performance shares to be awarded in the form of common stock to certain participants of the plan. These performance shares vest based on the level of achievement of certain performance goals, including the incremental value achieved from the company’s high-protein and clean sugar initiatives, annual production levels and return on investment (ROI). Performance shares granted in 2025 and 2024 include certain market-based factors requiring a Monte Carlo valuation model to estimate the fair value of the performance shares on the date of the grant. The weighted average assumptions used by the company in applying the Monte Carlo valuation model for performance share grants and related valuation include a risk-free interest rate of 3.87 % and 4.44 %, dividend yields of 0 %, expected volatility of 55.4 % and 54.6 %, and closing stock price on the date of grant of $ 5.48 and $ 20.21 , resulting in an estimated fair value of $ 7.08 and $ 25.23 per share for 2025 and 2024, respectively. Off-cycle awards of performance shares occurred on August 19, 2025. A portion of the off-cycle awards contained certain market-based factors requiring a Monte Carlo valuation model to estimate the fair value of the performance shares on the date of the grant. The weighted average assumptions used in applying the Monte Carlo valuation model for off-cycle performance share awards include a risk free rate of 3.69 %, dividend yields of 0 %, expected volatility of 58.0 %, and closing price of the date of grant of $ 8.34 , resulting in an estimated fair value of $ 12.89 per share. Performance shares granted in 2023 do not contain market-based factors requiring a Monte Carlo valuation model. The performance shares were granted at a target of 100 %, but each performance share can be reduced or increased depending on results for the performance period. If the company achieves the maximum performance goals, the maximum amount of 31 Table of Contents shares available to be issued pursuant to the 2025, 2024 and 2023 awards are 962,030 performance shares which represents 200 % of the 481,015 performance shares which remain outstanding, excluding forfeited shares. The actual number of performance shares that will ultimately vest is based on the actual performance targets achieved at the end of the performance period. This excludes an additional 69,959 performance shares granted to the Chief Legal and Administration Officer and Corporate Secretary in 2023, 2024 and 2025, which will vest at 100 % of target on December 31, 2025. On March 14, 2022, the Compensation Committee of the Board granted performance shares to be awarded in the form of common stock to certain participants of the plan. The performance shares were granted at a target of 100 %, but each performance share was reduced or increased depending on results for the performance period. On March 14, 2025, based on the criteria discussed above, the 2022 performance shares vested at 30 %, which resulted in the issuance of 14,259 shares of common stock. On February 28, 2025, the company announced the departure of Todd Becker as President and Chief Executive Officer, effective March 1, 2025. In accordance with his separation agreement, 221,895 of remaining outstanding performance shares that were granted during 2022, 2023, and 2024 vested immediately at target. The non-vested performance share award activity for the nine months ended September 30, 2025, is as follows: Performance Shares Weighted- Average Grant- Date Fair Value Weighted-Average Remaining Vesting Term (in years) Non-Vested at December 31, 2024 538,572 $ 27.82 Granted 460,656 7.22 Forfeited ( 142,097 ) 25.86 Vested ( 306,157 ) 24.73 Non-Vested at September 30, 2025 550,974 $ 12.82 2.0 Stock-Based Compensation Expense Compensation costs for the stock-based payment plan were $ 2.6 million and $ 13.7 million for the three and nine months ended September 30, 2025, respectively, and $ 3.6 million and $ 10.2 million for the three and nine months ended September 30, 2024, respectively, with the increase primarily driven by accelerated vesting for the company's former CEO. At September 30, 2025, there was $ 10.8 million of unrecognized compensation costs from stock-based compensation related to non-vested awards. This compensation is expected to be recognized over a weighted-average period of approximately 2.1 years. The potential tax benefit related to stock-based payment is approximately 24.5 % of these expenses. 10. EARNINGS PER SHARE Basic earnings per share, or EPS, is calculated by dividing net income available to common stockholders by the weighted average number of common shares outstanding during the period. The company computes diluted EPS by dividing net income on an if-converted basis, adjusted to add back net interest expense related to the convertible debt instruments, by the weighted average number of common shares outstanding during the period, adjusted to include the shares that would be issued if the convertible debt instruments were converted to common shares and the effect of any outstanding dilutive securities. 32 Table of Contents The basic and diluted EPS are calculated as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 EPS - basic Net income (loss) attributable to Green Plains $ 11,926 $ 48,200 $ ( 133,218 ) $ ( 27,562 ) Weighted average shares outstanding - basic (1) 69,855 63,946 66,826 63,741 EPS - basic $ 0.17 $ 0.75 $ ( 1.99 ) $ ( 0.43 ) EPS - diluted Net loss attributable to Green Plains $ 11,926 $ 48,200 $ ( 133,218 ) $ ( 27,562 ) Interest and amortization on 2.25% convertible notes due 2027, net of tax effect 1,214 1,209 — — Net income (loss) attributable to Green Plains - diluted $ 13,140 $ 49,409 $ ( 133,218 ) $ ( 27,562 ) Weighted average shares outstanding - basic 69,855 63,946 66,826 63,741 Effect of dilutive 2.25% convertible notes due 2027 7,273 7,273 — — Effect of dilutive stock-based compensation awards 741 441 — — Weighted average shares outstanding - diluted 77,869 71,660 66,826 63,741 EPS - diluted $ 0.17 $ 0.69 $ ( 1.99 ) $ ( 0.43 ) Anti-dilutive weighted-average convertible debt, certain warrants and stock-based compensation (2) — — 7,910 7,687 (1) For the three and nine months ended September 30, 2025, weighted average shares outstanding - basic includes the impact of 750,000 warrants outstanding as of September 30, 2025 that have an exercise price of $ 0.01 . (2) For the nine months ended September 30, 2025 and 2024, respectively, the effects related to the company's 2.25 % convertible notes due in 2027, certain warrants and certain stock-based compensation awards were excluded from diluted EPS as the inclusion of these shares would have been anti-dilutive. 11. STOCKHOLDERS’ EQUITY BlackRock Warrants During the three months ended March 31, 2021, in connection with certain agreements, the company issued 2,000,000 warrants in a private placement to purchase shares of its common stock. The company entered into an amendment on its Junior Notes on May 7, 2025, and the warrants ("2029 warrants") were repriced from $ 22.00 to $ 0.01 and the maturity date extended from April 28, 2026 to December 31, 2029. The warrants were revalued on May 7, 2025, and the increase in fair value was recorded in additional paid-in capital. On August 10, 2025, in conjunction with extending the maturity date of the Junior Notes, 3,250,000 warrants ("2035 warrants") were issued with an exercise price of $ 0.01 and a maturity date of August 10, 2035. Of the total, 2,500,000 of these warrants were equity-based and the fair value of the warrants was recorded in additional paid-in capital, and 750,000 were liability-based and the fair value of warrants was initially recorded in other liabilities. On August 18, 2025, 1,250,000 of the 2029 warrants and 750,000 of the 2035 warrants were exercised. On September 8, 2025, the remaining 2,500,000 2035 warrants were fully exercised and the fair value of the liability-based warrants was reclassified from other liabilities to additional paid-in capital. The company recognized $ 2.0 million of expense due to the revaluation of liability-based warrants, which was recorded in other, net on the consolidated statements of operations 33 Table of Contents during the three and nine months ended September 30, 2025. At September 30, 2025, 750,000 of the 2029 warrants remain outstanding. Ancora Warrants On May 7, 2025, in connection with a revolving credit facility agreement, the company issued warrants in a private placement to purchase 1,504,140 shares of its common stock at an exercise price of $ 0.01 per share and expiration date of May 7, 2035. The company measured the fair value of the warrants as of the issuance date. These warrants were equity-based and recorded in additional paid-in capital. On August 29, 2025, all of the Ancora warrants were exercised and none remained outstanding. Other Warrants Other warrants issued in 2021 totaling 550,000 have a strike price of $ 22.00 . The expiration dates are December 8, 2025 for 275,000 warrants and February 9, 2026 for 275,000 warrants. Of the total, 275,000 of the warrants, of which 222,222 are exercisable as a result of achieving certain earn-out provisions and 52,778 are contingent upon certain earn-out provisions, are treated as liability-based awards, and valued quarterly using the company’s stock price. The other 275,000 are equity-based, are all exercisable, and remain outstanding. These warrants could potentially dilute basic earnings per share in future periods. Green Plains Partners Merger As a result of the Merger, for the nine months ended September 30, 2024, the company issued approximately 4.7 million shares of common stock and recorded par value $ 0.001 per share, paid cash consideration of $ 29.2 million, extinguished the non-controlling interest attributed to the partnership common units held by the public of $ 133.8 million, and capitalized transaction costs of $ 7.5 million, within additional paid-in capital. Refer to Note 3 - Merger and Dispositions included herein for more information. Components of stockholders’ equity for the three and nine months ended September 30, 2025 and 2024 are as follows (in thousands): 34 Table of Contents Common Stock Additional Paid-in Capital Retained Deficit Accumulated Other Comprehensive Loss Treasury Stock Total Green Plains Stockholders' Equity Non- Controlling Interests Total Stockholders' Equity Shares Amount Shares Amount Balance, December 31, 2024 67,512 $ 68 $ 1,213,646 $ ( 318,298 ) $ 973 2,805 $ ( 31,174 ) $ 865,215 $ 9,322 $ 874,537 Net loss — — — ( 72,906 ) — — — ( 72,906 ) 265 ( 72,641 ) Other comprehensive loss before reclassification — — — — ( 2,307 ) — — ( 2,307 ) — ( 2,307 ) Amounts reclassified from accumulated other comprehensive loss — — — — 37 — — 37 — 37 Other comprehensive loss, net of tax — — — — ( 2,270 ) — — ( 2,270 ) — ( 2,270 ) Investment in subsidiaries — — — — — — — — 94 94 Stock-based compensation 688 — 7,468 — — — — 7,468 — 7,468 Balance, March 31, 2025 68,200 68 1,221,114 ( 391,204 ) ( 1,297 ) 2,805 ( 31,174 ) 797,507 9,681 807,188 Net loss — — — ( 72,238 ) — — — ( 72,238 ) 11 ( 72,227 ) Other comprehensive loss before reclassification — — — — ( 8,191 ) — — ( 8,191 ) — ( 8,191 ) Amounts reclassified from accumulated other comprehensive loss — — — — 2,747 — — 2,747 — 2,747 Other comprehensive loss, net of tax — — — — ( 5,444 ) — — ( 5,444 ) — ( 5,444 ) Investment in subsidiaries — — — — — — — — 94 94 Proventus disposition — — — — — — — — ( 4,534 ) ( 4,534 ) Issuance of warrants — — 5,656 — — — — 5,656 — 5,656 Modification of warrants — — 7,520 — — — — 7,520 — 7,520 Stock-based compensation 193 — 2,179 — — — — 2,179 — 2,179 Balance, June 30, 2025 68,393 68 1,236,469 ( 463,442 ) ( 6,741 ) 2,805 ( 31,174 ) 735,180 5,252 740,432 Net loss — — — 11,926 — — — 11,926 ( 952 ) 10,974 Other comprehensive loss before reclassification — — — — ( 12,105 ) — — ( 12,105 ) — ( 12,105 ) Amounts reclassified from accumulated other comprehensive loss — — — — 5,831 — — 5,831 — 5,831 Other comprehensive loss, net of tax — — — — ( 6,274 ) — — ( 6,274 ) — ( 6,274 ) Investment in subsidiaries — — — — — — — — 1,726 1,726 Issuance of warrants — — 18,475 — — — — 18,475 — 18,475 Exercises of warrants 6,276 6 7,576 — — — — 7,582 — 7,582 Stock-based compensation 65 1 2,033 — — — — 2,034 — 2,034 Balance, September 30, 2025 74,734 $ 75 $ 1,264,553 $ ( 451,516 ) $ ( 13,015 ) 2,805 $ ( 31,174 ) $ 768,923 $ 6,026 $ 774,949 35 Table of Contents Common Stock Additional Paid-in Capital Retained Deficit Accumulated Other Comprehensive Loss Treasury Stock Total Green Plains Stockholders' Equity Non- Controlling Interests Total Stockholders' Equity Shares Amount Shares Amount Balance, December 31, 2023 62,327 $ 62 $ 1,113,806 $ ( 235,801 ) $ ( 3,160 ) 2,805 $ ( 31,174 ) $ 843,733 $ 146,323 $ 990,056 Net loss — — — ( 51,412 ) — — — ( 51,412 ) 290 ( 51,122 ) Other comprehensive loss before reclassification — — — — ( 6,043 ) — — ( 6,043 ) — ( 6,043 ) Amounts reclassified from accumulated other comprehensive loss — — — — 5,305 — — 5,305 — 5,305 Other comprehensive loss, net of tax — — — — ( 738 ) — — ( 738 ) — ( 738 ) Investment in subsidiaries — — — — — — — — 166 166 Partnership Merger 4,746 5 97,035 — — — — 97,040 ( 133,765 ) ( 36,725 ) Stock-based compensation 349 — ( 1,169 ) — — — — ( 1,169 ) — ( 1,169 ) Balance, March 31, 2024 67,422 67 1,209,672 ( 287,213 ) ( 3,898 ) 2,805 ( 31,174 ) 887,454 13,014 900,468 Net loss — — — ( 24,350 ) — — — ( 24,350 ) 312 ( 24,038 ) Other comprehensive loss before reclassification — — — — ( 657 ) — — ( 657 ) — ( 657 ) Amounts reclassified from accumulated other comprehensive loss — — — — 1,748 — — 1,748 — 1,748 Other comprehensive income, net of tax — — — — 1,091 — — 1,091 — 1,091 Investment in subsidiaries — — — — — — — — 167 167 Stock-based compensation 39 — 3,173 — — — — 3,173 — 3,173 Balance, June 30, 2024 67,461 67 1,212,845 ( 311,563 ) ( 2,807 ) 2,805 ( 31,174 ) 867,368 13,493 880,861 Net loss — — — 48,200 — — — 48,200 437 48,637 Cash dividends and distributions declared — — — — — — — — — — Other comprehensive income before reclassification — — — — 338 — — 338 — 338 Amounts reclassified from accumulated other comprehensive loss — — — — 6,052 — — 6,052 — 6,052 Other comprehensive income, net of tax — — — — 6,390 — — 6,390 — 6,390 Investment in subsidiaries — — — — — — — — ( 481 ) ( 481 ) Stock-based compensation ( 4 ) — 3,554 — — — — 3,554 — 3,554 Balance, September 30, 2024 67,457 $ 67 $ 1,216,399 $ ( 263,363 ) $ 3,583 2,805 $ ( 31,174 ) $ 925,512 $ 13,449 $ 938,961 Amounts reclassified from accumulated other comprehensive loss are as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, Statements of Operations Classification 2025 2024 2025 2024 Gains (losses) on cash flow hedges Commodity derivatives $ ( 1,169 ) $ 5,146 $ ( 1,194 ) $ 8,882 (1) Commodity derivatives ( 6,627 ) ( 13,088 ) ( 10,325 ) ( 26,109 ) (2) Total losses on cash flow hedges ( 7,796 ) ( 7,942 ) ( 11,519 ) ( 17,227 ) (3) Income tax benefit 1,965 1,890 2,904 4,122 (4) Amounts reclassified from accumulated other comprehensive loss $ ( 5,831 ) $ ( 6,052 ) $ ( 8,615 ) $ ( 13,105 ) (1) Revenues (2) Costs of goods sold (3) Income (loss) before income taxes and income (loss) from equity method investees, net of income taxes (4) Income tax benefit 36 Table of Contents 12. INCOME TAXES The company records actual income tax expense or benefit during interim periods rather than on an annual effective tax rate method. Certain items are given discrete period treatment and the tax effect of those items are reported in full in the relevant interim period. The IRA was signed into law on August 16, 2022. The IRA includes significant law changes relating to tax, climate change, energy and health care. The IRA significantly expands clean energy related tax credits and permits more flexibility for taxpayers to use the credits with direct-pay and transferable credit options. The OBBB was signed into law on July 4, 2025. The OBBB includes a broad range of tax reform provisions affecting businesses, including extending and modifying certain key provisions of the Tax Cuts & Jobs Act, and expanding certain Inflation Reduction Act incentives while accelerating the phase-out of others. Important business provisions of the OBBB include reinstatement of permanent expensing of domestic research and development costs, higher EBITDA cap on the deduction for interest expense and 100% bonus depreciation. In addition, the OBBB extends the tax credit for Clean Fuel Production under Section 45Z to December 31, 2029, and leaves credits generated from carbon capture under Section 45Q substantially unchanged. The company expects to benefit from the business provisions of the OBBB and the extension of certain energy credits under the IRA and not be negatively impacted by the phase-out of other energy credits. The company will benefit from the reinstatement of permanent expensing of domestic research and development costs and the higher EBITDA cap on the deduction for interest expense, as well as the extension of the tax credit for Clean Fuel Production under Section 45Z to December 31, 2029. The Section 45Z clean fuel production credit is a general business credit under Section 38 that is allowed with respect to clean transportation fuel produced domestically after December 31, 2024, and before December 31, 2029. This credit, which was part of the Inflation Reduction Act of 2022, and subsequently extended by the OBBB, incentivizes the production of clean fuels at our plants that reduce GHG emissions below a CI score of 50. The tax credit is calculated by multiplying the gallons of clean transportation fuel produced times the CI emission factor times the applicable credit rate per gallon ($0.20 for non-SAF transportation fuel, or $1.00 if the taxpayer satisfies the prevailing wage requirements under Section 45). The company expects that it is more-likely-than-not that prevailing wage requirements will be met for 2025 for six facilities and has calculated the credit at the highest credit rate. On September 16, 2025, the company entered into an agreement, pursuant to which the company agreed to supply production tax credits available under Section 45Z to a buyer from the production of the company's ethanol at its Nebraska facilities between January 1, 2025 and December 31, 2025. Under the agreement, the company expects to deliver up to $ 65 million worth of credits, upon satisfaction of certain conditions. The final proceeds are dependent on actual production and the final CI score at the company's facilities. Based on production and CI scores for the nine months ended September 30, 2025, the company recorded an income tax benefit of $ 26.5 million, net of a valuation allowance, related to 45Z production tax credits. The company expects to benefit from certain energy related tax credits in future years. On January 9, 2024, the transactions contemplated by the Merger Agreement were completed as described in more detail in Note 3 - Merger and Dispositions included herein. For income tax purposes, the total consideration given by the company in exchange for the remaining interest in the partnership, creates a tax basis in the acquired interest. Because the GAAP basis in the acquired interest is less than the total consideration, a new deferred tax asset was created. The company's valuation allowance on deferred tax assets increased by a corresponding amount, which did not have a material impact on the company's consolidated financial statements. The effective tax rate can be affected by variances in the estimates and amounts of taxable income among the various states, entities and activity types, realization of tax credits, adjustments from resolution of tax matters under review, valuation allowances and the company’s assessment of its liability for uncertain tax positions. 13. COMMITMENTS AND CONTINGENCIES Leases The company leases certain facilities, parcels of land, and equipment, with remaining terms ranging from less than one year to approximately 12.1 years. The land and facility leases include renewal options. The renewal options are included in the lease term only for those sites or locations in which they are reasonably certain to be renewed. Equipment renewals are not considered reasonably certain to be exercised as they typically renew with significantly different underlying terms. 37 Table of Contents The components of lease expense are as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Lease expense Operating lease expense $ 7,526 $ 7,173 $ 22,339 $ 21,272 Variable lease expense (1) 683 551 1,009 1,234 Total lease expense $ 8,209 $ 7,724 $ 23,348 $ 22,506 (1) Represents amounts incurred in excess of the minimum payments required for a certain building and land leases and for the handling and unloading of railcars offset by railcar lease abatements provided by the lessor when railcars are out of service during periods of maintenance or upgrade. Supplemental cash flow information related to operating leases is as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2025 2024 2025 2024 Cash paid for amounts included in the measurement of lease liabilities Operating cash flows from operating leases $ 7,688 $ 7,540 $ 22,683 $ 21,737 Right-of-use assets obtained in exchange for lease obligations Operating leases 6,169 7,753 11,017 17,491 Right-of-use assets and lease obligations derecognized due to lease modifications: Right-of-use assets (1) 3,739 2,208 3,739 2,208 Lease obligations (1) 3,739 2,739 3,739 2,739 (1) Amounts presented in 2025 are related to the Obion Transaction, while amounts in 2024 relate to the Birmingham Transaction. Derecognition of right-of-use assets and lease obligations for both dispositions is related to railcar operating leases. Supplemental balance sheet information related to operating leases is as follows: September 30, 2025 December 31, 2024 Weighted average remaining lease term 3.7 years 4.0 years Weighted average discount rate 5.50 % 5.36 % 38 Table of Contents Aggregate minimum lease payments under the operating lease agreements for the remainder of 2025 and in future years are as follows (in thousands): Year Ending December 31, Amount 2025 $ 6,787 2026 21,852 2027 17,618 2028 9,144 2029 5,612 Thereafter 6,155 Total 67,168 Less: Present value discount ( 6,583 ) Lease liabilities $ 60,585 Other Commitments As of September 30, 2025, the company had contracted future purchases of grain, distillers grains and natural gas valued at approximately $ 152.9 million and future commitments for storage and transportation, valued at approximately $ 30.3 million. During the second quarter of 2025, the company entered into a product financing arrangement with a financial institution in which it received up front payment for corn oil that the company has an obligation to repurchase in weekly increments through January of 2026. As of September 30, 2025, a liability of $ 20.9 million was recorded within product financing arrangement on the consolidated balance sheets. The company has entered into contracts with Tallgrass High Plains Carbon Storage, LLC and its affiliates, related to the construction, development and operation of carbon capture and sequestration projects at our three Nebraska plants, which are expected to meet in-service requirements in the fourth quarter of 2025. Payments associated with these contracts are due monthly over a period of twelve years , commencing after the capture facilities are considered in-service. Amounts due under the contracts are based on the achievement of certain project milestones and are subject to termination of all or portions of the contracts. Certain of the future obligations to Tallgrass High Plains Carbon Storage LLC are secured by a leasehold deed of trust, security agreement and assignment of rents and leases. As of September 30, 2025, the company had incurred $ 117.5 million of accumulated construction costs in relation to the projects, presented as property, plant and equipment on the consolidated balance sheet, with offsetting liability presented as carbon equipment liabilities on the consolidated balance sheets. We currently estimate that annualized payments would total $ 17.8 million. Legal The company is currently involved in litigation that has arisen in the ordinary course of business, but does not believe any pending litigation will have a material adverse effect on its financial position, results of operations or cash flows. 14. SUBSEQUENT EVENTS CCS Commencing Operations CCS equipment at our York, Nebraska, plant began operations on October 14, 2025, and is delivering biogenic carbon dioxide to the Tallgrass Trailblazer pipeline for permanent sequestration. Successful sequestration will allow the company to further reduce its CI, triggering an increase in the amount of income tax benefit recognizable from 45Z production tax credits in future periods. Convertible Debt Exchange On October 27, 2025, the company executed separate, privately negotiated exchange agreements with certain of the holders of its existing 2.25 % Convertible Senior Notes due 2027 (or the “2027 Notes”) to exchange (or the “exchange transactions”) $ 170 million aggregate principal amount of the 2027 Notes for $ 170 million of newly issued 5.25 % Convertible Senior Notes due November 2030 (or the “2030 Notes”). Additionally, the company completed separate, privately negotiated subscription agreements pursuant to which it issued $ 30 million of 2030 Notes for $ 30 million in cash 39 Table of Contents (the “subscription transactions”). $ 200 million in aggregate principal amount of the 2030 Notes is now outstanding, and $ 60 million in aggregate principal amount of the 2027 Notes remains outstanding with existing terms unchanged. The company used approximately $ 30 million of the net proceeds from the subscription transactions to repurchase approximately 2.9 million shares of its common stock from certain holders participating in the subscription transactions. The 2030 Notes will bear interest at a rate of 5.25 % per year, payable on May 1 and November 1 of each year, beginning May 1, 2026. The notes will be general senior, unsecured obligations of the company. The initial conversion rate of the 2030 Notes is 63.6132 shares of common stock per $1,000 principal amount of 2030 Notes (equivalent to an initial conversion price of approximately $ 15.72 per share of common stock, which represents a conversion premium of approximately 50 % over the offering price of our common stock), and is subject to customary anti-dilution adjustments. 40 Table of Contents