Northern Chile is home to the world’s largest copper ore deposits, which have been exploited for thousands of years by different groups, at varying scales and for different purposes. In this context, it is important to develop new protocols to characterise the mineralogical variability of archaeological copper ores. A comprehensive and representative methodology in the analysis of minerals, the application of non-destructive analytical techniques, and the combination of insights from geological, archaeological and local knowledge are key to developing a copper mineral repository of the Atacama Desert area. Geochemical analyses were applied to the study of 568 samples from the archaeological site Pukara de Turi, with different techniques such as micro-XRF, XRD, QEMSCAN, Raman spectroscopy and technological studies. This exhaustive analysis allowed for the recognition of two mineralogical associations: atacamite/brochantite (99%) and azurite/chrysocolla (1%). The study of various minerals allows data to be interpreted more reliably and to trace the likely geological sources of these minerals. The azurite/chrysocolla samples appear to belong to the same mineral association found in the Cerro Verde district, which is probably the source of these samples. The atacamite/brochantite samples appear to come from more than one geological source, including, but not limited to, Chuquicamata-Radomiro Tomic and El Abra-Conchi.