The Zhubu Ni–Co–PGE sulfide deposit in the Permian Emeishan Large Igneous Province (LIP), SW China is hosted by a mafic–ultramafic intrusion that comprises two morphologically distinct ore-forming spaces: a central, layered sequence that represents a magma chamber surrounded by a marginal sub-vertical conduit zone. The marginal conduit zone contains significant Ni–Co–PGE sulfide mineralization, suggesting that high volumes of sulfide-bearing silicate melt flowed through the magma conduit system. Determining the hosts of Co is key to understanding the Co enrichment process in the Zhubu deposit, as well as in the Emeishan LIP as a whole. We assess this here using the geochemistry and Fe–S isotope compositions of sulfides in the Zhubu deposit. Cobalt is mainly concentrated in pentlandite sulfide in the websterite, with Co contents increasing in the order pyrrhotite < chalcopyrite < pyrite < pentlandite < violarite; the abundance of violarite, however, is notably lower than that of the other sulfides. The Co contents of pentlandite, pyrite, and chalcopyrite are negatively correlated with their Ni and Fe contents, suggesting that Co substitutes isomorphically for Ni and Fe in the sulfide structure. The δ56Fe values of sulfides increase in the order pyrrhotite < chalcopyrite < pentlandite < pyrite resulted from kinetic fractionation of Fe isotopes. The δ56Fe values of pentlandite and chalcopyrite in lherzolite are higher than those in websterite, implying that lherzolite and websterite formed in compositionally distinct magmas, Fe isotope compositions become heavier with crystal fractionation. The δ34S values of sulfides increase in the order pyrrhotite < pentlandite < chalcopyrite < pyrite, similar to the fractionation sequence of sulfide melts, suggesting that externally derived S was added to the magma and contributed to its sulfide saturation. The Co contents of chalcopyrite and pyrite vary positively with δ56Fe values, and negatively with δ34S values, indicating that the addition of externally derived S and resulting sulfide segregation were critical to Co enrichment.