Heavy metals are chemical contaminants, toxic, potentially carcinogenic and/or mutagenic, stable, persistent and are of concern in the food chain. The risk to the consumer of the presence of inorganic arsenic (iAs), cadmium (Cd), chromium (Cr), mercury (Hg) and lead (Pb) in five varieties (Bourbon, Típica, Catimor, Caturra and Pache) of parchment coffee from five regions (Amazonas, Cajamarca, Cusco, Huánuco and San Martín) was investigated in this study. A predictive model of the stages of coffee bean hulling, roasting and infusion was built to simulate the process. The results by region showed significant differences in which San Martín had the highest iAs, Cr and Pb values. The variety was only significant for Cr, of which Pache presented the highest concentration. The Cd and Hg values were below the detection limits. The hazard index (HI) was less than 1 for iAs, Cd, Cr and Hg and the combination of margin of exposure and the probability of exceedance (MOE-POE) for Pb indicated that an adverse health effect was not likely. The cancer risk (CR) for iAs and Pb in the 95th percentile was considered as both high and acceptable, respectively.