Petroleum-bearing fluid inclusions are small encapsulations of oil and gas that persist in the rock record long after their parent fluids have moved on. The chemical and isotopic compositions of inclusions offer a unique way to investigate hydrocarbon formation pathways in deep Earth environments and in ancient geological times. Here we use stable isotope compositions of methane, including clumped isotopologues 13CH3D and 12CH2D2, to evaluate the formation conditions of methane within fluid inclusions in Alpine tectonic quartz fissures. We observe that this CH4 is relatively 13C and 2H enriched (δ13C = −26 to −39‰; δ2H = −126 to −146‰), consistent with the formation by advanced catagenesis of organic matter, and has clumped isotope compositions indicating intramolecular isotopic equilibrium at catagenetic to low-grade (sub-greenschist) metamorphic temperatures (TΔ13CH3D: 120-300°C; TΔ12CH2D=2120-260°C). Our findings, combined with an analysis of the geographic distributions of inclusion-bearing fissures and fluid inclusion PVT behaviors, provide direct evidence of reservoirs of thermogenic methane trapped beneath the Alps during Mid-Miocene tectonic nappe emplacement (c.a. 25 to 15 Ma). The gas was sequestered in a concentrated form that likely favored the accumulation of up to 50,000-150,000 Megatons (Mt) of CH4 across the Helvetic domain in Switzerland. Following the subsequent tectonic uplift during the period 17 to 10 Ma, we suggest that the trapped methane-rich fluids migrated to shallower depths along faults, leading to the release of Alpine metamorphic methane into near-surface aquifers and the atmosphere at rates of 0.01 to 0.03 Mt⋅y−1.