Understanding diagenetic reactions in accreted sediments is critical for establishing the balance of fluid sources and sinks in accretionary prisms, which is in turn important for assessing the fluid pressure field and the ability for faults to host seismic slip. For this reason, we studied diagenetic reactions in deformation bands (shear zones and veins) within deep mud sediments from the Nankai accretionary prism (SW Japan) drilled at site C0001 during IODP Expedition 315, by means of microscopic observation, X-ray diffraction, and major-trace element analyses. Deformation bands are not only more compacted than the host sediment, but are also enriched in framboidal pyrite, as observed under microscopy and confirmed by chalcophile element enrichments (Fe, S, Cu, As, Sb, Pb). In tandem, clays in deformation bands undergo a destabilization of smectite or illite/smectite mixed layers, and/or a slight crystallization of illite, which is matched by a correlated increase in B and Li compared to the host sediment. The two diagenetic reactions of sulfide precipitation and clay transformation are both explained by a combined action of sulfate-reducing and methanogen bacteria, which strongly suggests an increased activity of anaerobic microbial communities localized in deformation bands. This local bacterial proliferation was possibly enhanced by the liberation of hydrogen from strained phyllosilicates. We suggest that the proliferation of anoxic bacteria, boosted by deformation, may participate in the pore water freshening observed at depth in accretionary prisms. Deformation-enhanced metabolic reactions may also explain the illitization observed in major faults of accretionary prisms. Care is therefore needed before interpreting illitization, and other diagenetic reactions as well, as evidence of shear heating, as these might be biogenic instead of thermogenic.