Breaking Down Clean Energy Fuels Corp. (CLNE) Financial Health: Key Insights for Investors

You're looking at Clean Energy Fuels Corp. (CLNE) and seeing a complex picture-solid growth in core business but a widening bottom-line loss. Honestly, you're right to pause. The Q3 2025 results show a revenue beat, hitting $106.1 million, which is a clear sign that demand for their Renewable Natural Gas (RNG) is strong, with volumes up 3% to 61.3 million gallons sold. But, the net loss for the quarter expanded to $(23.8) million, a jump from the previous year, driven by factors like higher Amazon warrant charges and the expiration of the Alternative Fuel Tax Credit (AFTC). The big question is whether their strategic investments-like the new RNG production facilities-can convert that demand into sustainable profitability, especially when the nine-month net loss is already sitting at $(179.03) million. We defintely need to break down what these numbers mean for your investment strategy right now.

Revenue Analysis

You're looking at Clean Energy Fuels Corp. (CLNE) and trying to figure out where the money actually comes from, which is smart. The headline revenue numbers for 2025 can be a bit misleading because of a few non-cash and regulatory shifts. For the full 2025 fiscal year, the analyst consensus projects revenue to be around $405.59 million. That's a marginal increase over the prior year, but the underlying business is showing better momentum.

The core of Clean Energy Fuels Corp.'s business is selling fuel, specifically Renewable Natural Gas (RNG) and conventional natural gas, to large vehicle fleets across the U.S. and Canada. Think heavy-duty trucking, public transit, and airport shuttles. The revenue streams break down into three main buckets, and you need to look at all of them to get the full picture.

• Fuel Sales: The primary driver, measured in gallons sold.
• Credit Revenues: Income from environmental credits like Renewable Identification Numbers (RINs) and Low Carbon Fuel Standards (LCFS).
• Services/Construction: Revenue from building, operating, and maintaining fueling stations.

The year-over-year growth rate is a perfect example of why you must look past the GAAP (Generally Accepted Accounting Principles) top line. In the third quarter of 2025, Clean Energy Fuels Corp. reported $106.1 million in revenue, which was a slight increase over Q3 2024. But here's the kicker: the Alternative Fuel Tax Credit (AFTC) expired at the end of 2024. That credit contributed $6.4 million to Q3 2024 revenue, but $0.0 million in Q3 2025. So, when you strip out that non-recurring government credit, the underlying revenue from fuel sales and construction actually grew by about 8%. That's a defintely stronger signal for the base business.

The shift to RNG is a clear opportunity, and it's driving volume. The company sold 61.3 million gallons of RNG in Q3 2025, a 3% rise year-over-year. The second quarter saw even better volume growth, with 61.4 million RNG gallons sold, marking a 7.5% increase over Q2 2024. That's where the real value is being built.

You also need to understand the impact of the Amazon warrant. This is a non-cash contra-revenue charge that reduces the reported GAAP revenue, but it's actually a sign of success. The charge, which was $17.4 million in Q2 2025, is tied to the volume of fuel sold to Amazon.com NV Investment Holdings LLC. It reflects more fueling demand from Amazon, but it hits the revenue line negatively in the short term. The table below shows the quarterly revenue progression for 2025.

The takeaway here is simple: the core business of selling low-carbon fuel is growing, but regulatory changes and non-cash accounting items are masking that growth in the GAAP numbers. If you want to dive deeper into the full picture, check out the rest of the analysis in Breaking Down Clean Energy Fuels Corp. (CLNE) Financial Health: Key Insights for Investors.

Profitability Metrics

You're looking at Clean Energy Fuels Corp. (CLNE) because the renewable natural gas (RNG) space is booming-the market is projected to be worth over $15.20 billion in 2025. But for an investor, a growing market doesn't automatically mean profit. The short answer is that while CLNE is showing strong gross margin performance, its operating and net profitability remain deeply negative as of the third quarter of 2025.

Here's the quick math for the first nine months (9M) of 2025, which gives us the freshest look at the company's financial health. Through September 30, 2025, CLNE reported total revenue of $312.514 million. However, the drag from operating costs and one-time charges is significant, leading to a substantial net loss. The profitability picture is complex, so let's break it down by margin.

Gross Profit: A Strong Foundation

Clean Energy Fuels Corp.'s gross profit margin (GPM) is the brightest spot, demonstrating solid operational efficiency in its core business of selling RNG and related services. The company's latest twelve months (LTM) GPM stands at approximately 29.0%. This is a healthy figure and shows that the cost of goods sold (COGS) is well-managed relative to revenue. To be fair, this GPM is slightly lower than the 30.9% seen in the full fiscal year 2024, but it is in line with the Q3 2025 performance of some peers in the RNG sector, like Anaergia, which reported a 28.8% gross profit margin.

• Gross Margin is a measure of core efficiency.
• Latest GPM is near 29.0%.
• It suggests strong pricing power and cost management.

Operating and Net Profit Margins: The Cost Challenge

The real challenge for CLNE is what happens after gross profit-the operating expenses (OpEx) and non-operating items. For the 9M period ending September 30, 2025, CLNE incurred an operating loss of $(149.166) million. This translates into an Operating Margin of approximately -47.7%. This massive loss is driven by high selling, general, and administrative (SG&A) costs, and crucially, significant depreciation and amortization charges, including accelerated depreciation from the removal of LNG station assets.

The net profit margin (NPM) is even more concerning due to one-time, non-cash charges. For the same 9M 2025 period, the net loss attributable to Clean Energy Fuels Corp. was $(179.026) million, resulting in a Net Profit Margin of about -57.3%. The full-year 2025 GAAP net loss is projected to range from $220 million to $225 million, which includes a one-time $64.3 million goodwill impairment charge and an estimated $53 million in Amazon warrant expenses. This is a clear case where non-cash items skew the bottom line, but they still reflect real balance sheet adjustments.

Peer Comparison and Operational Efficiency

When we stack CLNE up against the industry, the high gross margin is a positive signal, but the negative bottom-line margins are the major differentiator. Other RNG players are showing a path to net profitability:

The table shows CLNE's operational efficiency (cost management beyond COGS) is lagging. The company is generating strong gross profit, but a significant portion of that profit is eaten up by SG&A and depreciation, plus those non-cash charges. This means the company needs to defintely focus on scaling its revenue base relative to its fixed costs, or aggressively cut its overhead. The good news is that management is guiding for an Adjusted EBITDA of $50 million to $55 million for 2025, which strips out those non-cash items and gives a cleaner view of cash flow from operations. This is where the underlying business strength is. You need to look closer at Mission Statement, Vision, & Core Values of Clean Energy Fuels Corp. (CLNE) to see their long-term strategy for closing this profitability gap.

Debt vs. Equity Structure

You're looking at Clean Energy Fuels Corp. (CLNE)'s balance sheet to understand how they fund their growth, and that's the right move. The short answer is they use a manageable mix, leaning slightly toward equity, but the debt structure is what you need to watch. The company's financial leverage, measured by its debt-to-equity (D/E) ratio, sits at about 0.65 as of the third quarter of 2025.

This 0.65 D/E ratio is defintely on the lower, safer side compared to the broader capital-intensive energy sector, where a ratio up to 2.0 is often considered acceptable. It means for every dollar of shareholder equity, Clean Energy Fuels Corp. is using about 65 cents of debt. For a company building out a massive Renewable Natural Gas (RNG) infrastructure, that's a relatively conservative approach to funding expansion.

Here's the quick math on their leverage components from the Q3 2025 balance sheet:

• Total Stockholders' Equity: $713.273 million
• Total Debt (Current & Long-Term): $305.327 million (approximately)
• Net Debt (March 2025): $45.0 million (Total Debt less Cash)

The total debt figure is comprised of a relatively small current portion of debt at $40 million due within the next year, and a long-term portion of $265.327 million. The low net debt is a key strength; it shows that their cash pile of $226.6 million (as of March 2025) could cover a significant chunk of their total obligations if they had to pay down debt quickly. That's a good sign of liquidity.

To be fair, this conservative D/E ratio doesn't mean the debt market is completely bullish. While analysts have a 'Moderate Buy' consensus on the stock, Weiss Ratings reaffirmed a 'sell (D-)' rating in October 2025, which reflects some underlying financial concerns, including profitability challenges.

Balancing Financing and Future Moves

Clean Energy Fuels Corp. balances its capital structure by relying on equity funding-including retained earnings and capital raised from stock offerings-to keep its long-term debt manageable. This is a common strategy for growth companies in a volatile sector, as it avoids high interest payments that can crush earnings when revenue is inconsistent.

Still, they are actively engaging the debt market for strategic growth. The company's 2025 10-K noted plans to manage its debt through refinancing and potential equity offerings. We've also seen talk of a potential Stonepeak $400 million Term Loan, which, if finalized, would be a major debt issuance aimed at accelerating their development of RNG production facilities. That kind of debt injection would temporarily spike the D/E ratio, but it's a calculated risk to fund high-growth, high-return RNG projects.

What this estimate hides is the true cost of their equity-based funding, specifically the impact of the Amazon warrant expenses, which can create a non-cash charge against net income. You need to consider both sides of the balance sheet. For more on the company's strategic vision that drives this capital allocation, check out their Mission Statement, Vision, & Core Values of Clean Energy Fuels Corp. (CLNE).

The takeaway is simple: the current debt load is low-risk, but keep a close eye on the details of any new debt issuance, like the Stonepeak loan, to see if the increased leverage is matched by a clear, high-return path for their RNG expansion.

Liquidity and Solvency

Clean Energy Fuels Corp. (CLNE) maintains a strong near-term liquidity position, which is defintely a key strength for a growth-focused company in the capital-intensive renewable natural gas (RNG) space. Your ability to cover short-term obligations is excellent, but you need to keep a close eye on the capital deployment pace in the investing cash flow, as that's where the future growth is being funded.

The core of a company's financial flexibility is its ability to meet immediate debts, and Clean Energy Fuels Corp. shows a healthy buffer. The current ratio and quick ratio tell the story here.

• Current Ratio: As of September 30, 2025, the Current Ratio stood at approximately 2.68. This means the company has $2.68 in current assets for every $1.00 in current liabilities. For a non-financial company, anything consistently above 1.5x is solid; 2.68x is a sign of operational comfort.
• Quick Ratio (Acid-Test Ratio): The Quick Ratio, which strips out inventory-an asset that can be slow to convert to cash-was approximately 2.39. This is still very high and signals that the company's most liquid assets, like cash and receivables, are more than sufficient to cover all its short-term debt.

Here's the quick math on the working capital (Current Assets minus Current Liabilities). It's the capital available for day-to-day operations. At the end of 2024, working capital was roughly $259.05 million, which saw a slight dip to approximately $256.73 million by the close of the third quarter of 2025. This small reduction is not a concern; it primarily reflects the normal ebb and flow of operations and strategic investment timing, not a structural liquidity issue. It's a very small change, so the trend is stable.

A deeper look at the cash flow statement, covering the trailing twelve months (TTM) ended September 30, 2025, shows where the money is moving and how it is being used to fund growth.

The TTM Cash Flow from Operations (CFO) of $94.28 million is a significant positive, indicating the core business is generating substantial cash, even with a GAAP net loss of $23.8 million for Q3 2025. This is a crucial distinction: the company is cash-flow positive from operations, which is what matters most for self-sustaining liquidity. The Investing Cash Flow (CFI) of -$17.10 million shows capital expenditure (CapEx) for expansion, which is expected for a company building out infrastructure like new RNG production facilities and fueling stations.

On the financing side, you see a mix. The company's total long-term debt increased slightly to $284.2 million as of Q3 2025, up from $265.3 million at the end of 2024. This is a manageable increase, especially considering the strong liquidity position. Plus, the company has resumed repurchasing shares, a sign of management's confidence and a way to return capital to shareholders. The combination of strong operating cash flow and a high current ratio means there are no immediate liquidity concerns. Still, investors should monitor the long-term debt-to-equity ratio, which is around 0.65 (TTM), a moderate level.

For a deeper dive into who is betting on this liquidity and growth strategy, check out Exploring Clean Energy Fuels Corp. (CLNE) Investor Profile: Who's Buying and Why?

Valuation Analysis

The core takeaway for Clean Energy Fuels Corp. (CLNE) is that traditional valuation metrics paint a mixed, but largely 'undervalued' picture right now, especially when looking at assets. The consensus from six analysts is a Moderate Buy as of November 2025, with an average price target that suggests significant upside from the current price of around $2.22.

You're looking at a growth-oriented clean energy play, so you need to look past a few red flags. The company's valuation is complicated by its current lack of profitability, but its asset-based metrics show a clear discount compared to its book value. This is defintely a case where cash flow and future earnings potential matter more than trailing earnings.

Is Clean Energy Fuels Corp. (CLNE) Overvalued or Undervalued?

Clean Energy Fuels Corp. is trading below its book value, which often signals an undervalued stock, but its negative earnings mean you must focus on Enterprise Value. The company's Price-to-Book (P/B) ratio sits at approximately 0.81 (TTM), meaning the market values the company at less than its net assets. This is a strong indicator of an undervalued stock from an asset perspective.

However, the Price-to-Earnings (P/E) ratio is negative, at around -2.47, because the company is not currently profitable, with a projected 2025 Earnings Per Share (EPS) of -$0.23. This is common for companies heavily investing in infrastructure and growth, like those focused on Renewable Natural Gas (RNG). The Enterprise Value-to-EBITDA (EV/EBITDA) ratio is high at around 54.5x (LTM as of September 30, 2025), which reflects the non-profitability and the market pricing in future earnings potential. Here's the quick math on the key ratios:

Stock Price Momentum and Analyst Targets

The stock price has been volatile over the last 12 months, which is typical for the clean energy sector. The 52-week trading range for Clean Energy Fuels Corp. has been a low of $1.30 and a high of $3.67. The recent closing price around $2.20 to $2.22 sits closer to the low end of that range, suggesting it has room to run if positive catalysts emerge.

The analyst community is optimistic, with a consensus 12-month price target of $3.59. This target implies an upside of over 60% from the current price, which is a substantial potential return if the company executes on its strategy, especially its focus on RNG. You can review their long-term strategy in detail here: Mission Statement, Vision, & Core Values of Clean Energy Fuels Corp. (CLNE).

Dividend Policy and Payout

For investors looking for income, Clean Energy Fuels Corp. is not a dividend stock. The company's dividend yield is 0.00% and its payout ratio is also 0.00%, meaning it retains all earnings to fund its growth and capital expenditures. This aligns with a company in a high-growth, capital-intensive industry, prioritizing expansion over shareholder distributions.

• Expect no dividends in the near term.
• Focus your analysis on capital appreciation.

Risk Factors

You need to look past the strong volume growth in renewable natural gas (RNG) and focus on the structural risks that keep Clean Energy Fuels Corp. (CLNE) in the red. The biggest challenges are regulatory volatility and the company's persistent struggle to translate sales into profit, a tension point that defines the stock right now.

Honestly, the profitability picture is tough. The net profit margin currently sits at -48.4%, which is miles below the U.S. Oil and Gas industry average of 14.8%. Analysts project continued losses for at least the next three years, so this isn't a near-term fix. Plus, revenue growth is expected to be around 7.9% per year, slower than the broader U.S. market's projected 10.5% yearly growth. Here's the quick math: you need faster growth or much higher margins to close that gap, and both are under pressure.

The core of the external risk is regulatory uncertainty, specifically around environmental credits. Clean Energy Fuels Corp. relies heavily on the value of Renewable Identification Numbers (RINs) and Low Carbon Fuel Standard (LCFS) credits to make its margins work. The EPA's proposed reduction in D3 RIN volume requirements, for example, caused D3 RIN prices to drop 24.3% in Q1 2025 alone, creating significant market uncertainty. Any shift in federal or state policy can immediately gut a key revenue stream.

You also have to watch the operational and non-cash financial risks highlighted in their 2025 filings:

• Project Ramp-Up Delays: Five out of six dairy RNG sites are still reporting losses, slowing the move to vertical integration and higher-margin supply.
• Non-Cash Charges: The Q1 2025 GAAP net loss widened dramatically to $(135.0) million, driven by a $(64.3) million goodwill impairment and $(50.7) million in accelerated depreciation from abandoned LNG stations.
• Customer Adoption: Sales of trucks equipped with the new, critical Cummins X15N engine have been slower than expected, which directly impacts future demand.
• Contract Renewal: The potential non-renewal of the agreement with Pilot Travel Centers, LLC, could force the abandonment and removal of assets at 55 stations, leading to significant accelerated depreciation expenses down the line.

To be fair, management is taking clear steps to mitigate these risks. They are actively pursuing joint ventures with partners like TotalEnergies and BP to secure RNG supply, a move that diversifies their sourcing and helps offset volatility. They are also using commodity swap contracts to hedge against price volatility, a necessary defense against the RIN and LCFS swings. Furthermore, the company resumed share repurchases in the first half of 2025, buying back nearly 4.9 million shares for $7.9 million, signaling confidence in their long-term value.

The company's strategy is to leverage its extensive fueling network and long-term contracts with transit agencies to create a resilient base. You can read more about that foundation here: Mission Statement, Vision, & Core Values of Clean Energy Fuels Corp. (CLNE).

What this estimate hides is that their revised 2025 Adjusted EBITDA guidance of $60-65 million is a non-GAAP metric that strips out those huge non-cash charges. This is defintely a high-risk, high-reward situation where policy and project execution will determine the outcome.

Growth Opportunities

You're looking for a clear path forward for Clean Energy Fuels Corp. (CLNE) beyond the current volatility, and the story is defintely centered on Renewable Natural Gas (RNG) and strategic infrastructure plays. The near-term risks, like regulatory uncertainty and the slower-than-expected rollout of new heavy-duty trucks, are real, but the company's core business model is built on a clear, growing trend: decarbonizing fleet transportation.

The company's management is confident, raising their full-year 2025 Adjusted EBITDA guidance to between $60 million and $65 million, up from earlier forecasts. This is an operational win, showing they are managing costs and driving higher-margin RNG volumes. Here's the quick math: while the consensus 2025 revenue projection sits around $422 million, the focus should be on the quality of that revenue-specifically, the shift to RNG, which generates valuable credits like Low Carbon Fuel Standard (LCFS) and Renewable Identification Numbers (RINs).

Key Growth Drivers and Product Innovation

The primary driver is the accelerating adoption of RNG, which is essentially biogas captured from organic waste, a fuel that can achieve a negative carbon intensity score. This makes it a premium product in the low-carbon fuel market. The company is positioned to capitalize on this through several avenues:

• Heavy-Duty Trucking: The new Cummins X15N natural gas engine is a major catalyst. While sales have been slower than anticipated, this engine is expected to drive significant future adoption in the heavy-duty trucking market, offering fleets a 2-2.5-year payback period due to lower fuel costs.
• RNG Production Expansion: Clean Energy Fuels is moving toward vertical integration. They are actively developing dairy RNG projects, with two large projects in Texas and Idaho on schedule to begin producing RNG by the end of 2025. This shift reduces reliance on external suppliers and improves margin control.
• Hydrogen Diversification: They are starting to diversify their product line. In a move that signals future product innovation, the company was awarded a contract in November 2025 to design and build a new hydrogen fueling station for Gold Coast Transit District, a project backed by $12.1 million from the U.S. Department of Transportation.

Strategic Partnerships and Market Expansion

Clean Energy Fuels' strategy is to lock in recurring revenue with large, stable customers. They do this by leveraging their infrastructure advantage, which is their biggest competitive moat. They have the largest RNG fueling network in the country, boasting over 550 fueling stations. No one else can ensure a steady flow of this clean fuel like they can.

Recent contracts in 2025 underscore this strategy. New partnerships with transit agencies, including the Los Angeles Metro, Trinity Metro in Texas, and the City of El Paso, are expected to deliver over 20 million gallons of RNG annually. This focus on public transit and municipal fleets (over 9,000 transit buses are fueled daily at 115 locations) provides a resilient base. Also, their joint venture with BP, CE bp Renew Co, LLC, successfully monetized $29.5 million in Investment Tax Credits (ITCs) in the first half of 2025, injecting capital directly into their RNG development projects.

What this estimate hides is the potential impact of regulatory changes, like the 45Z tax credit, which could significantly boost the economics of their RNG projects. The company's full-year 2025 GAAP net loss is still projected to be substantial, ranging from $212 million to $217 million, largely due to non-cash charges like depreciation and goodwill impairment from older assets. The operational picture is improving, but the accounting loss remains a headwind.

For more on the long-term vision driving these partnerships, you should review the company's stated goals: Mission Statement, Vision, & Core Values of Clean Energy Fuels Corp. (CLNE).

2025 Financial Projections Snapshot

To give you a clear picture of the near-term financial outlook, here is a summary of the key 2025 fiscal year consensus estimates and company guidance:

Next step: Have your team model the impact of a 10% increase in X15N engine adoption on 2026 RNG volume by the end of the month.