Although natural gas generates lower CO2 emissions, gas extraction, processing, and distribution all release methane, which has a greater global warming potential than CO2. Biomethane and biogas that use organic wastes as a feedstock have emerged as alternatives to natural gas, with lower carbon and methane emissions. However, the extent to which methane is still emitted at various stages along biogas and biomethane supply chains remains unclear. Here, we adopt a Monte Carlo approach to systematically synthesize the distribution of methane emissions at each key biomethane and biogas supply chain stage using data collected from the existing literature. We show that the top 5% of emitters are responsible for 62% of emissions. Methane emissions could be more than two times of greater than previously estimated, with the digestate handling stage responsible for the majority of methane released. To ensure the climate benefits of biomethane and biogas production, effective methane-mitigation strategies must be designed and deployed at each supply chain stage.