Native metals and metal alloys are common in serpentinized ultramafic rocks, generally representing the redox and sulfur conditions during serpentinization. Variably serpentinized peridotites from the Santa Elena Ophiolite in Costa Rica contain an unusual assemblage of Cu-bearing sulfides and native copper. The opaque mineral assemblage consists of pentlandite, magnetite, awaruite, pyrrhotite, heazlewoodite, violarite, smythite and copper-bearing sulfides (Cu-pentlandite, sugakiite [Cu(Fe,Ni)8S8], samaniite [Cu2(Fe,Ni)7S8], chalcopyrite, chalcocite, bornite and cubanite), native copper and copper–iron–nickel alloys. Using detailed mineralogical examination, electron microprobe analyses, bulk rock major and trace element geochemistry, and thermodynamic calculations, we discuss two models to explain the formation of the Cu-bearing mineral assemblages: (1) they formed through desulfurization of primary sulfides due to highly reducing and sulfur-depleted conditions during serpentinization or (2) they formed through interaction with a Cu-bearing, higher temperature fluid (350–400 °C) postdating serpentinization, similar to processes in active high-temperature peridotite-hosted hydrothermal systems such as Rainbow and Logatchev. As mass balance calculations cannot entirely explain the extent of the native copper by desulfurization of primary sulfides, we propose that the native copper and Cu sulfides formed by local addition of a hydrothermal fluid that likely interacted with adjacent mafic sequences. We suggest that the peridotites today exposed on Santa Elena preserve the lower section of an ancient hydrothermal system, where conditions were highly reducing and water–rock ratios very low. Thus, the preserved mineral textures and assemblages give a unique insight into hydrothermal processes occurring at depth in peridotite-hosted hydrothermal systems.