The presence of chemical contaminants in agricultural products is a continued food-safety challenge in Peru. This country has robust agriculture potential, but its output of fruits and vegetables is severely impacted by massive mining activities, as well as poor farming practices, including the use of polluted irrigation water, misuse of pesticides, and inadequate postharvest conditions. This review examines the current scientific knowledge on the levels of pesticide residues, heavy metals, and mycotoxins on crops produced in Peru. The available data shows that several crop varieties are contaminated with these classes of chemical contaminants, and at levels that exceed the national and international permissible limits. The abundance of chemical contaminants in produce indicates a relevant food-safety issue, which increases the risks of chronic human diseases, like cancer—a leading cause of death in Peru. Finally, this review presents recommendations to address these contamination problems in produce grown in the Andean country.