The relationship between microbial activity and the supergene modification of ore systems has been a major subject of debate. Here, we present isotopic evidence of microbial-driven secondary copper mineralization in the active cementation zone of the Las Cruces deposit, a volcanogenic massive sulfide deposit located in Iberian Pyrite Belt, Spain. Copper isotopic data show that the lower isotopic ratios (δ65Cu ≈ −9.2 ± 0.11 ‰, the lowest value measured worldwide in a supergene environment) are found in the upper part of the cementation zone, the same zone where the maximum copper grades are found and where there is direct evidence of extremophilic microbial activity. There is a tendency towards higher values downwards through the cementation zone (−9.2 ± 0.11 ‰ to + 1.67 ± 0.11 ‰ δ65Cu) and upwards into the former Cu-depleted gossan that originally capped the cementation zone (−7.79 ± 0.11 ‰ to −1.32 ± 0.11 ‰ δ65Cu). As microbes preferentially sequester the lighter isotope when incorporating intracellular Cu, this distribution indicates that microbes played a major role in the formation of the high-grade zones. Water arrives to the deposit enriched in isotopically heavy copper, likely because it has leached other ore bodies upstream. δ65Cu values of water currently flowing into the system are remarkably more positive than those in the ore, indicating that microbial activity is a major cause of copper isotope fractionation. At least half of the copper transported by the incoming waters remains within the ore body. Our best interpretation is that the large and high-grade cementation zone at Las Cruces is of biogenic origin, and that the primary mineralization acted as a trap for copper transported by groundwater, leading to the formation of an exotic mineralization distal to sub-eroded massive sulfides located upstream.