Manure Digesters Help Cut Methane — But They Also Leak

California, the United States’ top dairy producer, is heavily investing in manure digesters to curb methane emissions from its dairy farms. These systems are touted for breaking down cattle manure and other organic matter in an oxygen-free environment, capturing methane and converting it into clean energy.

But new research suggests these systems are leaking methane, a potent greenhouse gas — sometimes in volumes large enough to limit their climate benefits. Analyses from other researchers have also suggested that manure digesters are less effective than earlier, more optimistic analyses estimated, and need to be paired with other strategies for curbing greenhouse gas emissions from the dairy industry.

Researchers tracked methane emissions at 98 California dairies from 2016 to 2024 using satellite and airborne observations, comparing levels before, during and after manure digesters were installed. While methane emissions fell by 25% on average, the digesters themselves emerged as the largest source of emissions post installation, the study found. The research was published in Environmental Research Letters on March 24.

The findings highlight the need to monitor manure biodigesters, where they are used, and quickly alert operators to methane leaks. “When they leak or they don’t work effectively, they can create large amounts of methane that might turn it into a greenhouse gas problem, instead of a solution,” Alyssa Valdez, a PhD candidate at University of California, Riverside and the lead author of the study, tells Sentient.

Despite this concern, Valdez sees manure digesters as a useful tool when closely monitored, just not a standalone solution to the dairy industry’s contribution to the climate crisis.

Digester Leaks

Methane — which traps heat far more effectively than carbon dioxide over short periods of time — makes up 12% of the United States’ greenhouse gas emissions. In California, around 71% of agricultural greenhouse gas emissions come from livestock, mainly methane emissions from cattle digestion and manure management. Cutting methane at its source “can actually make a big impact and it might be a change we see in our lifetime,” much faster than some other climate solutions, Valdez says.

To address the methane problem, many states, including California, have turned to manure biodigesters. Microbes inside these biodigesters break down organic materials and produce biogas, mainly methane and carbon dioxide. Carbon dioxide is released into the atmosphere, while methane is captured and piped away to generate electricity, heat or fuel.

As of May 2025, California had 243 dairy manure biodigester projects in use or development, many funded by the state. The state’s Low Carbon Fuel Standard program has also helped drive expansion by rewarding fuels with lower carbon intensity than gasoline and diesel, such as biofuel. Some critics say the program entrenches industrial-scale livestock operations, while others argue that accounting methods can make digesters appear more effective than they really are.

Most of the state’s dairy cows and Concentrated Animal Feeding Operations (CAFOs) are clustered in the Central Valley. Valdez, who lived there for years, was struck by the air pollution and food insecurity in one of the country’s most productive agricultural regions. Her asthma meant that she struggled on days with poor air quality. That experience shaped her research focus: greenhouse gas emissions from dairies and manure management strategies. “There’s some cracks in the system that I really want to investigate,” she realized.

Her study found that methane emissions fell in about two-thirds of dairies after manure digesters — specifically covered lagoons — were installed. Covered lagoons are earthen pits where manure is stored and sealed with covers that capture the methane they release.

However, after installation, manure digesters became the “most persistent emitters” — representing 47% of plumes — compared with other on-farm sources such as lagoons, gas-handling systems and structures that house cows, according to the paper. While leaks were rare, they were also exceptionally potent: some exceeded 1,000 kilograms of methane per hour. By comparison, emissions from open lagoons typically ranged from 20 to 100 kilograms per hour.

Methane emissions from manure digesters can come from several sources. A California Air Resources Board analysis found that some came from leaks, some from intentional venting when systems exceed capacity or during processing and some during maintenance.

Another key finding of the study is the spikes observed in methane emissions during construction, Valdez says. Researchers observed higher and more frequent methane releases during installation than before or after. Though temporary, the construction phase can disrupt manure management and create new pathways for methane to escape. Digging lagoons and installing covers can also disrupt manure flow. Valdez suggests monitoring this period closely and ensuring it does not drag on.

There is a climate case for addressing methane leaks, but it makes economic sense too. “Leaks are also bad for the pockets of those who want to fund and build digesters,” Valdez says, noting that a digester company expressed interest in her findings.

The findings of the new study align with other research on digesters’ role in climate mitigation. A working paper from the World Resources Institute and a peer-reviewed study from Johns Hopkins University published last year suggest that while digesters can reduce odor and some methane, there are also ongoing concerns about leaks and increased emissions of ammonia and other pollutants.

Overhyped Solution or Useful Tool?

The benefits of manure digesters are “vastly overstated,” argues Brent Kim, one of the authors of the John Hopkins paper. He says that even a 25% reduction in methane emissions may give an inflated picture, since it only addresses one part of dairy’s climate footprint: manure management. Digesters do not address most greenhouse gas emissions from dairy, he says — such as those from land use, growing feed crops, raising animals and spreading manure.

Early findings from a preprint that has not been peer-reviewed also suggest that digesters may encourage larger dairy operations, because they incentivize farms to grow larger to produce more manure for biogas.

“The additional greenhouse gas emissions from larger herd sizes further undercut the already-modest reductions from digesters,” Kim says. His previous research similarly notes that investments in manure digesters can support the expansion of large-scale animal agriculture and fossil fuel infrastructure, both of which are linked to environmental and public health harms.

Kim adds that the buildout of digesters “diverts resources away from proven climate solutions and incentives growth in an industry in need of wholesale reform.”

Valdez argues against dismissing the technology entirely, though she believes that they should be part of a diverse set of tools for reducing dairy emissions. “Digesters have to be paired with other solutions and you have to continuously monitor them,” she says.