Tropical fruits are in high demand for their flavor and for their functional composition because these compounds are considered nutraceuticals. Passion fruit production is of economic importance to Ecuador; however, several Passiflora species are grown and each has to be analyzed to identify their phytochemical composition. In this study, the polyphenol, flavonoid, carotenoid, vitamin C, sugar and organic acid contents were determined. Six different Passiflora spp. germplasms were analyzed, coming from Passiflora edulis f. flavicarpa, Passiflora alata, Passiflora edulis f. edulis and unidentified Passiflora species (local germplasm). Measurement techniques included reflectometry for vitamin C, spectrophotometry for antioxidant compounds and HPLC for sugars and organic acids. Data were analyzed by principal component analysis, correlation and analysis of variance. Results showed that INIAP 2009 and P10 showed a high amount of polyphenols, antioxidant activity and citric content. Sweet passion fruit had the lowest vitamin C content while Gulupa showed the highest content. In terms of the local germplasm, POR1 showed the lowest content of flavonoids while PICH1 had high flavonoid and carotenoid content. Polyphenols were the main compounds that influenced antioxidant activity. This phytochemical information adds value to passion fruit as a nutraceutical source.