© The Author(s) 2020. The Puna-Altiplano plateau represents a regionally significant dust source, which is critically located at the nexus between the tropical and sub-polar synoptic systems that dominate the South American climate. Dust emissions in this region would therefore be expected to be sensitive to changes in these systems, in particular the strength and position of the South American Summer Monsoon (SASM). Here, we present a late-Holocene multi-proxy study where changes in dust flux, reconstructed from a high-altitude peat mire, are examined in light of climate variability and human impacts. Results show that for most the 4300 cal. yr BP record, dust flux sensitively tracked changes in SASM activity. Prior to 2600 cal. yr BP relatively high dust flux implies dry conditions prevailed across the Puna-Altiplao in association with reduced SASM activity. The chemistry of dust deposited at this time matched the large endorheic basins on the Puna, which host ephemeral lakes and terminal fans, indicating these were actively supplying dust to the airstream. After 2600 cal. yr BP, SASM activity increased while dust flux decreased and the dust chemistry changed, collectively implying the shutting down of the Puna-Altiplano as a significant dust source. Dust flux increased after 1000 cal. yr BP during the ‘Medieval Warm Period’, associated with a return to drier conditions and reactivation of dust sources across the endorheic basins of the Puna. Natural variability in dust flux was dwarfed, however, by the very significant increase in flux after 400 cal. yr BP following Spanish Colonisation and associated changing landuse practices. This finding attests to the globally significant role of humans on dust emissions.