Due to the great variations in altitude, humidity, hours of exposure to the sun, chemical and microbiological composition of the soil, the Andean and Amazon regions of Peru have a great diversity of microclimates, thus allowing the development of a wide variety of species of plants producing edible fruits. In addition to their nutritional value, these fruits are characterized by the presence of high levels of compounds beneficial to health, particularly polyphenols, such as flavonoids, lignans, phenolic acids, and stilbenes, and natural pigments, such as betalains. Several studies have shown that these compounds have antioxidant, antimicrobial, antitumor, and immunogenic activities and, therefore, can contribute to the prevention of diseases such as cancer, diabetes, and hypertension. Given the accumulated evidence, we believe that the consumption of fresh fruits from these regions, or even those preserved through industrial processes that maintain their properties, should be strongly encouraged. This manuscript aims to present and discuss the literature relevant to the benefits of consuming fruits from the Amazon and Andean regions of Peru for health maintenance.