Biogeochemical processes in subseafloor sediments can notably change over geological timescales due to variations in oceanographic, climatic and/or depositional conditions. To improve the understanding of changing biogeochemical processes on longer timescales, we investigated ~1.2 km deep and up to 120°C hot subseafloor sediments from the Nankai Trough offshore Japan (Site C0023), drilled during International Ocean Discovery Program Expedition 370 (Temperature Limit of the Deep Biosphere off Muroto)1. Over the past 15 Ma, the sediments have moved several hundreds of kilometers from the Shikoku Basin to the Nankai Trough due to tectonic motion of the Philippine Sea plate2. During this migration, the depositional, geochemical and thermal conditions have significantly changed. By combining geochemical data, sedimentation rates and reactive transport modeling, we reconstructed the evolution of biogeochemical processes in sediments at Site C0023. A distinctive feature at Site C0023 is an inverse sulfate-methane transition (SMT) at ~730 m depth with a broad sulfate-methane overlap zone of ~100 m, suggesting inefficient anaerobic oxidation of methane (AOM). This depth interval corresponds to a temperature of 80° to 85°C, which coincides with the known temperature limit of AOM-performing microbial communities3,4. Our model results demonstrate that the inverse SMT was formed at ~2.5 Ma after the onset of biogenic methanogenesis and AOM as a consequence of enhanced organic carbon burial. Depth-integrated AOM rates derived from the model markedly decrease since the beginning of trench-style deposition and the associated rapid heating of the sediments at ~0.4 Ma, indicating that the microbial activity of AOM-performing communities at the inverse SMT has already started to cease and the SMT is about to disappear. This successive fading of the SMT and, thus, a decrease in the efficiency of the microbial methane sink is ultimately related to the temperature increase beyond the threshold of being suitable for AOM-performing microbial communities. 1Heuer et al., (2017), In Proc. IODP Volume 370. 2Mahony et al., (2011), GSA Bulletin 123, 2201-2223. 3Holler et al., (2011), ISME J 5, 1946-1956. 4Biddle et al., (2012), ISME J 6, 1018-1031.