Pitahaya has originated worldwide interest due to its content of bioactive compounds with proven beneficial effects on health, acting as antioxidants against free radicals. This study aimed to evaluate the nutraceutical potential of the peel and pulp of the red (Hylocereus monacanthus) and yellow (Hylocereus megalanthus) pitahaya ecotypes for nutritional formulation purposes. Two pitahaya ecotypes were analyzed, obtaining a methanolic extract of the peel and edible part to perform the proximal chemical analysis, the phytochemical screening, and determine antioxidant activity by the DPPH, ABTS, and IC50 methods. Flavonoids, tannins, quinones, among other bioactive compounds, were identified. Yellow pitahaya presented higher content of polyphenols and higher antioxidant activity by the ABTS method, while the average inhibition percentage for both ecotypes was 93% by DPPH method. IC50 was higher for the edible part of red pitahaya with 1.68 mg mL-1. Both ecotypes have a high content of polyphenols and a high antioxidant capacity, which agree with those found in different studies such as those of Colombia, Brazil and Korea, being as high or even higher than most varieties of citrus fruits in Peru. Future studies should consider the inclusion of other metabolites and bioactive substances such as betalains due to their antioxidant activity. Both pitahaya ecotypes are rich in antioxidants, bioactive compounds, have low energy density, and may be suitable for food prescriptions as a functional ingredient in food industry.