Microorganisms produce and consume methane in terrestrial surface environments, sea sediments and, as indicated by recent discoveries, in fractured crystalline bedrock. These processes in the crystalline bedrock remain, however, unexplored both in terms of mechanisms and spatiotemporal distribution. Here we have studied these processes via a multi-method approach including microscale analysis of the stable isotope compositions of calcite and pyrite precipitated in bedrock fractures in the upper crust (down to 1.7 km) at three sites on the Baltic Shield. Microbial processes have caused an intriguing variability of the carbon isotopes in the calcites at all sites, with d13C spanning as much as −93.1‰ (related to anaerobic oxidation of methane) to +36.5‰ (related to methanogenesis). Spatiotemporal coupling between the stable isotope measurements and radiometric age determinations (micro-scale dating using new high-spatial methods: LA-ICP-MS U–Pb for calcite and Rb–Sr for calcite and co-genetic adularia) enabled unprecedented direct timing constraints of the microbial processes to several periods throughout the Phanerozoic eon, dating back to Devonian times. These events have featured variable fluid salinities and temperatures as shown by fluid inclusions in the calcite; dominantly 70–85 °C brines in the Paleozoic and lower temperatures (<50–62 °C) and salinities in the Mesozoic. Preserved organic compounds, including plant signatures, within the calcite crystals mark the influence of organic matter in descending surficial fluids on the microbial processes in the fracture system, thus linking processes in the deep and surficial biosphere. These findings substantially extend the recognized temporal and spatial range for production and consumption of methane within the upper continental crust.