AbstractMicroorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high‐level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site‐specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron‐reducing bacteria were predominant in comparison to methanogenic archaea and sulfate‐reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site‐specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low‐active mineral‐associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.