In carbonate rocks, natural production of sulfuric acid can form karstic cavities. Where both epigenic and hypogenic speleogeneses have taken place, these processes are challenging to constrain, especially if there is more than one source of sulfur involved. Thanks to an innovative approach coupling geomorphology with measurements of multiple sulfur, oxygen, and strontium isotopes, our study of two French Pyrenean caves quantifies the relative influence of both microbial and thermochemical processes implied in sulfuric-acid production. Multiple sulfur isotopes reveal that sulfate speleothems derived from a mixing of microbial H2S in hydrothermal water and fossil thermochemical H2S previously trapped within the cave host rock. We quantify the percentages of biotic and abiotic sulfuric-acid speleogeneses that have taken place in these caves, paving the way for similar studies of other sulfuric-acid caves where usually only microbial activity has been considered.