The city of Cuernavaca has experienced a significant deterioration in air quality in recent years. Despite this situation, few studies in the region have constantly monitored this problem. The objective of this study was to determine the concentrations of heavy metals in PM2.5 in three representative sites of the city and estimate the risks posed to human health and the environment. The results revealed concentrations in the following order of abundance: Fe > Al > Mg > Zn > As > Ni > V > Pb > Mn. The EF indicated that As comes mainly from anthropogenic emissions; Zn, V, Pb, and Ni come from natural and anthropogenic sources; and Mn, Fe and Al have a natural origin derived from the soil. The Igeo, As, Pb and Zn were greater than five, followed by V and Ni, whose values ranged between two and three. The ecological RI was far greater than 600 in all cases. The HQ revealed that all values were below one, indicating that the health risk posed by exposure to ambient air is below that established by the USEPA. The Ni ILCR values for adults were 1.03 × 10−5, followed by 2.9 × 10−6 and 1.6 × 10−7 for Pb and As, respectively. For children, the values were in the following order: Pb (1.2 × 10−6), Ni (4.8 × 10−6) and As (7.5 × 10−6). These findings suggest that Cuernavaca’s air has moderate to heavy contamination levels, which must be taken into account by environmental authorities so that measurements can be taken to help reverse this situation.