Cocona fruits are a popular food and medicinal fruit used mainly in the Amazon and several countries of South America for the preparation of several food products such as drinks, jams and milk shakes. In this study five ecotypes of cocona native to Peru have been studied regarding their nutritional and antioxidants values plus antihyperlipidemic activities. Seventy bioactive compounds have been detected in Peruvian cocona ecotypes including several phenolic acids, aminoacids and flavonoids; of those six were spermidines, (peaks 1, 2, 25, 26, 38 and 39), thirteen were aminoacids, (peaks 3–9, 11–13, 16, 17, 22–24), eighteen flavonoids (peaks 28, 30–32 45,46, 48–53 56, 57, 61 and 64–66), twelve were phenolics (peaks 19, 21, 27, 29, 34, 35, 36, 42, 43, 44, 54, and 59), two carotenoids, (peak 62 and 63), eight were lipid derivatives (peaks 37, 55, 58, 60 and 67–70), one sugar (peak 47), four terpenes (peaks 33, 40, 41 and 47), two amides, (peaks 10 and 18), one aldehyde, (peak 15), and three saturated organic acids, (peaks 4, 5 and 20). Hypercholesterolemic rats administered with pulp of the ecotypes CTR and SRN9 showed the lowest cholesterol and triglyceride levels after treatment (126.74 ± 6.63; 102.11 ± 9.47; 58.16 ± 6.64; 61.05 ± 4.00 mg/dL, for cholesterol, triglycerides, high-density lipoprotein and low-density lipoprotein respectively, for the group treated with SRN9 pulp, and 130.09 ± 8.55; 108.51 ± 10.04; 57.30 ± 5.72; and 65.41 ± 7.68 mg/dL, for cholesterol, triglycerides, HDL and LDL lipoproteins respectively for the group treated with CTR pulp). The ecotypes proved to be good sources of natural antioxidants and their consumption represent an alternative for the prevention of atherosclerosis.