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Abstract The Duluth Complex (DC) contains sulfide‐rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally‐weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long‐term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally‐weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse unculturedKtedonobacteria,Acetobacteria, andActinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally‐weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide‐rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large‐scale mining operations.