The use of black chromophores, or colored chemical compounds, in pottery is a recurrent theme in post-Formative period ceramics within Andean archaeology. However, the chemical components of these and thus the potential health repercussions for potters during ceramic manufacture are unknown. To test this we analyzed the black stains and paint on Arica ceramics (n = 55) from several periods in northern Chile to assess the presence of manganese (Mn). This mineral can be highly toxic to humans, particularly through the inhalation of Mn dust particles and fumes. The analysis of 11 Formative ceramic containers (ca. 1500 BCE–500 CE) show the absence of Mn paint, which contrasts with the post-Formative ceramics (Middle to Late Periods, n = 44, ca. 900–1530 CE) that reveal black Mn based paint was recurrently used to decorate post-Formative ceramics (Mn mean 19.8 %, range 4.41 % to 42.09 %). All post-Formative cultural periods (Middle to Late) showed Mn concentration greater than 15 %. We posit that the chaîne opératoire of Mn production (acquisition, grinding, painting, etc.) and possibly fumes during firing of pots most likely placed ancient Andean populations at occupational health risks. The potential hazards associated with Mn mining and firing pots need to be considered when investigating the ancient health and economic aspects of pre-Columbian ceramic production.