With the aim of understanding the mechanisms that control the metamorphic transition from the CH4– to the H2O–(CO2)-dominated fluid zone in the Helvetic domain of the Central Alps of Switzerland, fluid inclusions in quartz, illite “crystallinity” index, vitrinite reflectance, and the stable isotope compositions of vein and whole rock minerals and fluids trapped in quartz were investigated along four cross-sections. Increasing temperature during prograde metamorphism led to the formation of dry gas by hydrocarbon cracking in the CH4-zone. Fluid immiscibility in the H2O–CH4–(CO2)–NaCl system resulted in cogenetic CH4- and H2O-dominated fluid inclusions. In the CH4-zone, fluids were trapped at temperatures ≤270±5 °C. The end of the CH4-zone is marked by a sudden increase of CO2 content in the gas phase of fluid inclusions. At temperatures >270±5 °C, in the H2O-zone, the total amount of volatiles within the fluid decreased below 1 mol% with no immiscibility. This resulted in total homogenization temperatures of H2O–(CO2–CH4)–NaCl inclusions below 180 °C.Hydrogen isotope compositions of methane in fluid inclusion have δD values of less than −100‰ in the CH4-zone, typical for an origin through cracking of higher hydrocarbons, but where the methane has not equilibrated with the pore water. δD values of fluid inclusion water are around −40‰, in isotopic equilibrium with phyllosilicates of the whole rocks. Within the CH4 to H2O–(CO2) transition zone, δD(H2O) values in fluid inclusions decrease to −130‰, interpreted to reflect the contribution of deuterium depleted water from methane oxidation. In the H2O-zone, δD(H2O) values increase again towards an average of −30‰, which is again consistent with isotopic equilibrium with host-rock phyllosilicates. δ13C values of methane in fluid inclusions from the CH4-zone are around −27‰, in isotopic equilibrium with calcite in veins and whole rocks. The δ13C(CH4) values decrease to less than −35‰ at the transition to the H2O-zone and are no longer in equilibrium with the carbonates in the whole rocks. δ13C values of CO2 are variable but too low to be in equilibrium with the wall rock fluids, compatible with a contribution of CO2 from closed system oxidation of methane.Differences in isotopic composition between host-rock and Alpine fissure carbonate are generally small, suggesting that the amount of CO2 produced by oxidation of methane was small compared to the C-budget in the rocks and local pore fluids were buffered by the wall rocks during precipitation of calcite within the fissures.