We report results from comprehensive mapping and multi-technique geochemical characterization of obsidian from the Alca source in the Peruvian Andes (15.3°S, 72.7°W), aimed at understanding patterns of extraction and trade in one of the world’s centers of complex civilization. Alca obsidian was among the most economically important and widely distributed volcanic glasses used for stone tool making in South America from ca. 13 ka until recently, yet the geologic source of this material has never been studied comprehensively. Our work establishes Alca as one of the largest obsidian sources in South America and the only Peruvian source known to have patterned intrasource geochemical variability. There are six geochemically distinct Alca subsources exposed from 2710 to 5165 m elevation over >330 km2 of the highlands, an area nearly seven times larger than previously known. Our results now permit provenance determination of artifacts to specific outcrops. We analyzed 252 geologic samples using energy-dispersive X-ray fluorescence, neutron activation analysis, wavelength-dispersive X-ray fluorescence, and nondestructive, portable energy-dispersive X-ray fluorescence. All techniques distinguish the same six Alca subsources, establishing analytical comparability between geochemical methods. Discrimination of Alca obsidian to the subsource level using portable X-ray fluorescence represents a major advance in nondestructive provenance analysis. Further nondestructive analysis of robust sets of obsidian artifacts within Peru will allow high-resolution study of the evolution of central Andean exchange systems.