Although stone surfaces seem unlikely to be habitable, they support microbial life. Life on these surfaces are subjected to many varying harsh conditions and require the inhabitants to exhibit resistance to environmental factors including UV irradiation, toxic metal exposure, and fluctuating temperatures and humidity. Here we report the effect of hosting stone geochemistry on the microbiome of stone ruins found in Tamil Nadu, India. The microbial communities found on the two lithologies, granite and granodiorite, hosted distinct populations of bacteria. Geochemical composition analysis of sampled stones revealed quartz mineral content as a major driver of microbial community structure, particularly promoting community richness and proportions of Cyanobacteria and Deinococcus-Thermus. Other geochemical parameters including ilmenite, albite, anorthite, and orthoclase components or elemental concentrations (Ti, Fe, Mn, Na, and K) also influenced community structure to a lesser degree than quartz. Core members of the stone microbiome community found on both lithologies were also identified and included Cyanobacteria (Chroococcidiopsaceae and Dapisostemonum CCIBt 3536), Rubrobacter, and Deinococcus. A cluster of taxa including Sphingomonas, Geodermatophilus, and Truepera were mostly found in the granodiorite samples. Community diversity correlated with quartz mineral content in these samples may indicate that the microbial communities that attach to quartz surfaces may be transient and regularly changing. This work has expanded our understanding of built-stone microbial community structure based on lithology and geochemistry.