The hydrothermal caves linked to active faulting can potentially harbour subterranean atmospheres with a distinctive gaseous composition with deep endogenous gases, such as carbon dioxide (CO2) and methane (CH4). In this study, we provide insight into the sourcing, mixing, and biogeochemical processes involved in the dynamic of deep endogenous gas formation in an exceptionally dynamic hypogenic karst system (Vapour Cave, southern Spain) associated with active faulting. The cave environment is characterized by a prevailing combination of rising warm air with large CO2 outgassing (>1%) and highly diluted CH4 with an endogenous origin. The δ13CCO2 data, which ranges from −4.5 to −7.5‰, point to a mantle-rooted CO2 that is likely generated by the thermal decarbonation of underlying marine carbonates, combined with degassing from CO2-rich groundwater. A pooled analysis of δ13CCO2 data from exterior, cave, and soil indicates that the upwelling of geogenic CO2 has a clear influence on soil air, which further suggests a potential for the release of CO2 along fractured carbonates. CH4 molar fractions and their δD and δ13C values (ranging from −77 to −48‰ and from −52 to −30‰, respectively) suggest that the methane reaching Vapour Cave is the remnant of a larger source of CH4, which was likely generated by microbial reduction of carbonates. This CH4 has been affected by a postgenetic microbial oxidation, such that the gas samples have changed in both molecular and isotopic composition after formation and during migration through the cave environment. Yet, in the deepest cave locations (i.e., 30 m below the surface), measured concentration values of deep endogenous CH4 are higher than in atmospheric with lighter δ13C values with respect to those found in the local atmosphere, which indicates that Vapour Cave may occasionally act as a net source of CH4 to the open atmosphere.