Clean Energy Fuels Corp. (CLNE) stock intrinsic value fair value estimate & owner earnings analysis

What the business is. Clean Energy Fuels sells natural gas, mostly renewable natural gas (RNG) captured from dairies and landfills, as a truck and bus fuel. At the end of 2025 it owned, operated or supplied 582 fueling stations in 43 states and the District of Columbia, including more than 200 in California, plus 27 in Canada. It serves more than 1,200 fleet customers in refuse collection, public transit, heavy-duty trucking, airports and government. In 2025 it sold 300.1 million gallon-equivalents of fuel, 237.4 million of them RNG. It also builds stations for customers and runs maintenance on stations it does not own. About 98% of 2025 revenue of $424.8 million was booked in the United States and the rest in Canada. A large part of the profit comes from government environmental credits earned when RNG goes into a vehicle tank: federal Renewable Fuel Standard credits (RINs, $32.2 million of revenue in 2025) and low-carbon fuel credits in California, Oregon, Washington and New Mexico ($13.1 million). What the business actually earns. We measure owner earnings: the cash the business produces after stock compensation and the spending needed to keep its stations running, with year-to-year working-capital swings taken out. Over the last ten years this has been thin and often negative. It was negative in five of the ten years. The positive years from 2018 to 2021 were propped up by the federal alternative fuel tax credit, worth $20 million to $47 million a year. That credit expired on December 31, 2024 and has not been renewed. 2025 was the first year without the credit, and it was also the best year: owner earnings of about $37.1 million, or $0.17 per share. The first half of 2026 came in at about $17 million, compared with about $19 million in the first half of 2025. We treat about $34 million a year, roughly $0.155 per share, as the business's current earning power. Years before 2025 describe a business that was receiving a tax credit it no longer gets. Accounting judgements that matter. (1) Revenue is reduced every year by a non-cash charge for a warrant given to Amazon in 2021 ($66.1 million in 2025, and the company expects about $47 million in 2026). The warrant was a one-time payment in stock to win Amazon's fueling business. The charge spreads that 2021 cost over Amazon's fuel purchases, so we do not deduct it again from cash earnings. The real remaining cost to shareholders is dilution. Amazon can acquire up to about 58.8 million shares at $13.49 each until April 2031, and a lender, Stonepeak, holds warrants for 20 million shares at $5.50 and $6.50. All of these exercise prices are above our estimates of value in every case, so we assume no dilution. (2) Capital spending jumped to $100.9 million in 2023 and $65.0 million in 2024, mostly for station building and repairs at the Pickens LNG plant, yet total fuel volume grew only from 288.2 million gallons in 2023 to 300.1 million in 2025. Our year-by-year figures count that spending as a cost. For the forward view we use about $25 million a year, which matches the company's 2026 plan ($25.0 million) and the 2016-2021 average of $24.8 million. (3) Spending on dairy RNG plants and joint ventures with bp and TotalEnergies is kept separate. The results so far have been poor: $365.6 million invested through 2025, including $283.9 million put into joint ventures, produced only about 2.7 million gallons in 2025, and the company booked $26.7 million of losses from these ventures that year. (4) 2025 reported losses included a $64.3 million write-off of all goodwill and $54.4 million of accelerated depreciation after Pilot Travel Centers did not renew its LNG station agreement, which expired August 1, 2025. Neither was a cash cost. Base case ($1.38 per share). Owner earnings start at about $33 million over the next year. That is below 2025, consistent with the weaker first half of 2026 and less interest income as the cash pile shrinks. After that they grow about 2% a year to about $39 million in year ten. That growth rate rests on RNG volume growth of roughly 2.5% a year from 2023 to 2025 and on the company's report that fuel volume rose 7% year over year in the second quarter of 2026. Credit prices are held near today's levels. The company's plan to put up to $42 million into dairy RNG plants in 2026 is counted as money spent with no return credited, because the record so far shows none. Beyond year ten, earnings fade to zero over the following decade. The station network and fleet contracts are real and long-lived. But the credit programs are set by regulators, and California's push toward zero-emission trucks is disclosed in the filings as a long-term threat, so we do not assume the earnings last indefinitely. All cash flows are discounted at 6%. Bear case ($0.17 per share). Credit revenue falls back by about $10 million a year, toward the 2023 level ($35.7 million versus $45.3 million in 2025), so owner earnings fall to about $24 million. One customer, which we take to be Amazon, is more than 10% of revenue, and its warrant finishes vesting around 2028 (21.2 million unvested shares at the end of 2025, with 8.8 million vesting in 2025). From 2029 we assume that relationship shrinks. That costs about $8 million a year on our own margin estimate. The $250 million Stonepeak loan, which carries 9.5% interest and comes due in 2029, is refinanced at about $5 million a year more interest. Earnings then drift down 3% a year and end by year fifteen. RNG spending continues at $42 million, $30 million and $20 million over three years with no return, in line with the $48 million to $99 million a year put into RNG from 2021 to 2025. The business is still worth a little in this case, but almost nothing is left for shareholders. Bull case ($2.77 per share). Owner earnings start at about $36 million and grow 4% a year. The wholly owned South Fork dairy plant in Dimmitt, Texas came online in late 2025 with capacity of about 2.6 million gallons a year, and the six bp joint-venture projects are rated at up to 8.5 million gallons. We assume these ramp up and add about $8 million a year. The federal clean fuel production credit (Section 45Z) adds about $5 million a year from 2027 to 2029. The July 2025 tax law changed this credit, and the company says the change may let it keep benefiting. On its second-quarter 2026 call the company put the credit's value at up to about $5 million a year, pending final Treasury rules. Earnings hold for years eleven to twenty, then fade out by year twenty-five. What would make this wrong. The whole value rests on one good year, 2025, and one half-year of confirmation. If 2026 owner earnings come in well below about $30 million, the base case is too high. Environmental credit prices are set by regulators and have swung widely: RIN revenue went from $25.9 million to $39.0 million to $32.2 million over 2023 to 2025. The 2029 loan maturity is the main balance-sheet risk. Cash and short-term investments were $156.1 million at the end of 2025, less than the debt. On the upside, if the dairy RNG plants finally earn real returns, value would move toward the bull case. One item could not be fully reconciled from the annual report: a $26.8 million payment in the first half of 2026 to acquire additional interests in subsidiaries. We treated it as investment spending, not an operating cost.