Porphyry Cu-Au ore deposits are globally associated with convergent margins. However, controls on the processing and distribution of the chalcophile elements (e.g., Cu) during convergent margin magmatism remain disputed. Here, we show that magmas feeding many Chilean stratovolcanoes fractionate sulfides with a high-Cu/Ag ratio early in their crustal evolution. These magmas show evidence of lower-crustal garnet and amphibole crystallization, and their degree of sulfide fractionation and Cu depletion increase with both crustal thickness and the extent of garnet fractionation. However, samples from a small proportion of volcanoes with elevated eruptive fluxes depart from this Cu-depleting trend, instead erupting Cu-rich magmas. This implies that at these atypical sites, elevated magma productivity and crustal throughput, potentially facilitated by “pathways” exploiting major crustal fault systems, enable rapid magma transit, avoiding lower-crustal Cu-depleting sulfide fractionation and potentially playing an important role in porphyry ore genesis.