The Badami Caves are a significant example of ancient Indian rock-cut architecture, dating back to the 6th century. These caves are situated in the Malaprabha River valley and are part of the candidate UNESCO World Heritage Site known as the “Evolution of Temple Architecture—Aihole-Badami-Pattadakal”, which is considered to be the cradle of temple architecture in India. Our study aimed to investigate the diversity, distribution, and biodeterioration phenomena of the fungal communities present on the cave surfaces. The study also conducted a comprehensive analysis of fungal biodeterioration on the cave carvings. Utilizing specialized techniques, the dissolution of calcite, alterations in pH levels, and biomineralization capabilities of isolated fungal strains were monitored. Additionally, this study analyzed fungal acid production using high-performance liquid chromatography (HPLC). Our findings revealed that the major genera of fungi found on the cave surfaces included Acremonium, Curvularia, Cladosporium, Penicillium, and Aspergillus. These isolated fungi were observed to produce acids, leading to the dissolution of calcium carbonate and subsequent decrease in pH values. Notably, the dominant genus responsible for acid production and the promotion of biomineralization was Aspergillus. These discoveries provide valuable insight into the ecology and functions of fungi inhabiting stone surfaces, contributing to our understanding of how to preserve and protect sculptures from biodeterioration.