The Carboniferous-Permian organic-rich shale in the Karavanke/Karawanken tunnel exhibits extensive pyrite mineralization in the form of veins and impregnations. Significant thermal alteration, induced by the overlying Mesozoic rock sequences, led to the decomposition of organic matter into methane, which subsequently acted as a sulfate-reducing agent. The primary source of sulfate were the evaporitic layers hosted within the Paleozoic strata. Reduced sulfur species necessary for pyrite formation were produced through methane-mediated thermochemical sulfate reduction, catalyzed by specific cations (Ni2+, Fe2+) and clay minerals (montmorillonite). The mineralizing fluids originated from the expulsion of interstitial water and possibly from dehydration reactions related to the gypsum-to-anhydrite phase transition. The geochemical data indicate that the metals originated from the surrounding sedimentary rocks. These mineralizing fluids were characterized by low temperatures (< 300–350 °C), moderate reducing conditions, and low chlorinity. The low permeability of Carboniferous-Permian rocks, combined with the low trace element content of the investigated pyrite, mitigates the potential risk of environmental pollution.