The environmental credentials of Leon’s “carbon-neutral” burgers have been questioned after it emerged the fast-food chain was using controversial carbon offsets to make the claim.

In January, Leon announced it would become the first restaurant chain in the UK to serve carbon-neutral burgers and fries at more than 60 locations by reducing and offsetting the emissions they produce.

Alongside excluding high-carbon meats such as beef from its menu and using more sustainable energy sources, the company pledged to neutralise emissions by purchasing carbon credits from three rainforest conservation and tree-planting schemes.

But scientists and carbon market specialists have raised concerns about Leon’s claim and some of the credits they have used to substantiate their advertising.

One rainforest conservation project, the Peruvian Amazon, run by a partnership between two logging companies and a conservation NGO, was featured in a joint Guardian and Unearthed investigation that uncovered serious concerns about the project’s credibility.

The investigation found that the Redd+ (reducing emissions from deforestation and forest degradation) carbon credits, which are generated by preventing hypothetical deforestation, were unlikely to represent real emission reductions and threats to the forest had been overstated.

The findings at the time were fiercely criticised by Verra, a US non-profit that administers the world’s leading carbon credit standard, VCS (Verified Carbon Standard).

Britaldo Soares-Filho, a deforestation modelling expert and professor at the Institute of Geosciences at the Federal University of Minas Gerais in Brazil, whose software was used to model the hypothetical deforestation the project selected by Leon was preventing, warned they were “phantom credits” with little benefit to the climate.

“Beware of what you are eating: carbon neutrality of burgers sauced with Redd+ credits will not digest well,” he said.

Leon strongly disputed the claim it was using “phantom credits” and said it was confident the credits accredited by Verra helped “prevent greenhouse gas emissions, protect vital biodiversity and create sustainable livelihoods for forest communities”.

The company said it was aware of the Guardian’s investigation into the Madre de Dios project but was confident that the credits were helping to protect threatened rainforest.

Freya Chay, an analyst at CarbonPlan, a US organisation that scrutinises the credibility of climate solutions, said that while she sympathised with Leon, the company could not make a rigorous claim using the credits due to outstanding concerns about the project and the VCS standard, routinely used by other companies to make environmental claims.

“One common characteristic of Leon’s claim that stands out is how heavily it relies on the purported trustworthiness of third-party standards to establish offsets’ validity. Project credibility is based almost entirely on the third-party VCS seal of approval. This pattern is common and raises questions about who should be on the hook when offset credits turn out to be bad,” Chay said. “There’s no accountability, even when the problems are clear.”

“In this case, reporting has indicated significant concerns about the Madre de Dios project and the VCS standard under which it was credited, and VCS has apparently since changed its methodology to address a methodological shortcoming present in the Madre de Dios project. But as is the norm in these situations, the VCS methodological changes are forward-looking and don’t affect credits issued under existing projects.”

An increasing number of companies are using carbon credits to make environmental claims about their business practices, including airlines offering passengers the chance to “fly carbon neutral”, either by purchasing credits or doing so on their behalf.

James Dyke, the assistant director at the Global Systems Institute at the University of Exeter, said a burger could not be carbon neutral by virtue of purchasing offsets.

“First, offsetting schemes will not reduce atmospheric carbon now. Planting trees to take carbon out of the atmosphere will require years if not decades. Second, there are no assurances that carbon will stay locked up in a tree. Someone may come along and cut it down, or it could be burnt down during a wildfire,” he said.

“Third, some offsetting schemes are really promises to not be as destructive as we otherwise could be. So they are really about payments to protect existing forests from destruction. That doesn’t remove any carbon, it just tries to stop more of it entering the atmosphere.”

In a statement, Leon said sustainability was at the heart of its business and it had committed to be net zero by 2030. Carbon offsetting was just one part of its strategy to tackle unavoidable emissions, the company said, and the Madre de Dios project was one of many it supported.

Leon added: “Of the 13 burgers we’ve had on our menu this year, six have been vegan, giving our customers a wide range of naturally lower-carbon products to choose from.”

It also said the Madre de Dios project was one of many it backed.

A representative of the Madre de Dios project told the Guardian they disputed the findings of the previous investigation and were confident that their project was doing important work to prevent deforestation.