Soil is exposed to heavy metals that are associated with the anthropogenic activities, and is currently an environmental and food safety problem. The concentration and source of heavy metals in soils, the level of contamination and the potential for ecological risk in high Andean ecosystems were evaluated. The soil samples were collected from the surface part in which Andean crops were sown and the concentration of As, Cd, Pb, Fe and Zn was quantified. The concentrations of heavy metals in soils did not exceed the threshold of the national and international standard, while As, Pb and Zn exceeded the values of the background. The contamination factor (CF) values showed a high level of contamination for As and moderate for Pb and Zn. The geoaccumulation index (Igeo) values showed that As had the highest load of accumulated pollutants in soils by anthropogenic contribution. A moderate degree of contamination (CD) was found in 61.5% of the sampling sites. The potential ecological risk index (RI) showed that the soils of the study area presented a moderate to low potential ecological risk, and As was the main pollutant in high Andean soils. As, Pb and Zn occurring in high Andean soils mainly originated from human activities such as agricultural practices, whereas Fe mainly originated from the parent material of the soil. The effects of the use of organic and inorganic fertilizers on the accumulation of heavy metals in and Andean agricultural products must be analyzed and verified to protect the health of the inhabitants and the environment.