We present a comparative study between early, massive pyrite preceding (Cu–Ag) sulfosalt mineralization in high-temperature feeder zones (‘early pyrite’) and late pyrite that formed during silicic alteration associated with Au deposition (‘late pyrite’) at the El Indio high-sulfidation Au–Ag–Cu deposit, Chile. We use coupled in situ sulfur isotope and trace element analyses to chronologically assess geochemical variations across growth zones in these pyrite crystals. Early pyrite that formed in high-temperature feeder zones shows intricate oscillatory zonation of Cu, with individual laminae containing up to 1.15 wt% Cu and trace Co, As, Bi, Ni, Zn, Se, Ag, Sb, Te, Au, Pb and Bi. Late pyrite formed after (Cu–Ag) sulfosalt mineralization. It contains up to 1.14 wt% As with trace Cu, Zn, Pb, V, Mn, Co, Ni, Ge, Se, Ag, Sb, Te, Pb and Bi, as well as colloform Cu-rich growth bands containing vugs toward the outer edges of some crystals. Plotting the trace element data in chronological order (i.e., from core to rim) revealed that Co and Ni were the only elements to consistently co-vary across growth zones. Other trace elements were coupled in specific growth zones, but did not consistently co-vary across any individual crystal. The δ34S of early pyrite crystals in high-temperature feeder zones range from −3.19 to 1.88 ‰ (±0.5 ‰), consistent with sublimation directly from a high-temperature magmatic vapor phase. Late pyrite crystals are distinctly more enriched in δ34S than early pyrite (δ34S = 0.05–4.77 ‰, ±0.5 ‰), as a consequence of deposition from a liquid phase at lower temperatures. It is unclear whether the late pyrite was deposited from a small volume of liquid condensate, or a larger volume of hydrothermal fluid. Both types of pyrite exhibit intracrystalline δ34S variation, with a range of up to 3.31 ‰ recorded in an early pyrite crystal and up to 4.48 ‰ in a late pyrite crystal. Variations in δ34Spyrite at El Indio did not correspond with changes in trace element geochemistry. The lack of correlation between trace elements and δ34S, as well as the abundance of microscale mineral inclusions and vugs in El Indio pyrite indicate that the trace element content of pyrite at El Indio is largely controlled by nanoscale, syn-depositional mineral inclusions. Co and Ni were the only elements partitioned within the crystal structure of pyrite. Cu-rich oscillatory zones in early pyrite likely formed by nanoscale inclusions of Cu-rich sulfosalts or chalcopyrite, evidence of deposition from a fluid cyclically saturated in ore metals. This process may be restricted to polymetallic high-sulfidation-like deposits.