Background: Crassulacean acid metabolism plants, such as Stenocereus spp., are climate warming-resilient crops used as food and for by-products elaboration in arid and semi-arid agroecosystems. A few studies on secondary metabolites have been conducted in pitayo fruit (PF), but there are no reports of these compounds in juice powders (JP) with (JPS) or without seeds (JPWS). This study was devoted to characterizing the juice powders (JPS and JPWS) of five pitayas with different flesh colors with regard to some phytochemical and functional attributes. Methods: The study was conducted with a completely random design with factorial arrangement in treatments (PF × JP). Results: Differences among pitayas were related to peel and flesh color attributes. Except for soluble dietary fiber, the remainder of the non-digestible carbohydrates were greater in JPS than in JPWS of all pitayas. Phenols and flavonoids were found to be the highest in the JPWS of all pitayas, whereas total saponins were the highest in JPS of the ‘Pink’ pitaya. The JPWS of the ‘Yellow’ and ‘Reddish-Purple’ pitayas had the highest content of betaxanthins and indicaxanthins, respectively. Antioxidant capacity was the highest in JPS of ‘Reddish-Purple’ and ‘Pink’ pitayas. Conclusions: Except for some phenolic compounds, the study suggests that pitayas’ JPS would benefit human health when freshly consumed or as elaborated by-products.