Micellar microemulsions are thermodynamically stable self-emulsifying systems that have been used to successfully improve the low oral bioavailability of several bioactive phytochemicals, such as antioxidant polyphenols. However, most studies have reported the micellization of single-compounds or purified chemical fractions; thus, the stability, phytochemical-loading efficiency, and bioactivity of complex crude extracts remain largely unexplored. In this study, we evaluated the effects of micellar emulsification of tropical apple (Malus domestica cv. Anna), plum (Prunus domestica cv. Satsuma), and guava (Psidium guajava L.) extracts regarding particle size and stability, polyphenol-loading efficiency, antioxidant capacity, and cytotoxic activity in human and murine cells. Simple food-grade extraction protocols were implemented to obtain apple, plum, and guava extracts. Total polyphenols, flavonoids, and antioxidant activity (DPPH) were determined in the fruit extracts, and their polyphenol profile was further characterized by liquid chromatography (HPLC-DAD). The dried extracts were mixed into a food-grade, self-emulsifying system, and their cytotoxicity in human and murine cell lines was compared. Our research showed that complex fruit matrixes were successfully emulsified into thermodynamically stable polysorbate-based nanometric micelles with uniform size distribution and consistent pH stability, with potential applications in food and biomedical industries.