The formation of secondary copper deposits, the source of more than half of the world’s production, is usually interpreted as abiogenic. In this study of the Las Cruces deposit (southwestern Spain), in situ hybridization and scanning electron microscopy analysis together with integrated genomic and bioinformatic studies on cultures provide compelling evidence that a microbial community controls the current formation of the secondary copper mineralization. The cementation zone of this deposit contains abundant microbial life dominated by sulfate-reducing bacteria that coexist with methanogens and with other prokaryotes having unknown roles. Fractures in the primary massive sulfides are coated by extracellular polymeric substances in which the microbial cells are embedded. Covellite crystals have nucleated within these microbial aggregates, accreting and forming large crystals attached to the vein walls. These results strongly suggest that in situ microbial sulfate reduction can control the formation of secondary copper deposits. Equivalent processes could be widespread in similar deposits elsewhere, but they are probably overlooked due to the presumed low capability for fossilization of the microbes.