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Methane, a greenhouse gas and energy source, is commonly studied using stable isotope signals as proxies for its formation processes. In subsurface environments, methane often exhibits equilibrium isotopic signals, but the equilibration process has never been demonstrated in the laboratory. We cocultured a hydrogenotrophic methanogen with an H₂-producing bacterium under conditions (55°C, 10 megapascals) simulating a methane-bearing subsurface. This resulted in near-complete reversibility of methanogenesis, leading to equilibria for both hydrogen and carbon isotopes. The methanogen not only equilibrated kinetic isotope signals of initially produced methane but also modified the isotope signals of amended thermogenic methane. These findings suggest that hydrogenotrophic methanogenesis can overwrite the isotope signals of subsurface methane, distorting proxies for its origin and formation temperature—insights crucial for natural gas exploration.