Sacha inchi (Plukenetia huayllabambana) oil was microencapsulated by spray drying with gum arabic and with extracts of camu camu (Myrciaria dubia (HBK) Mc Vaugh) and mango (Mangifera indica) skins, obtained by assisted microwave. The physicochemical characteristics, such as moisture content, encapsulation efficiency, particle size, morphology, fatty acid composition and oxidative stability, were evaluated in order to select the best formulation for the development of functional foods. The most important results indicate that the microcapsules formulated with extracts of the fruit skins provide greater protection to sacha inchi oil (P. huayllabambana) against oxidation compared to commercial antioxidant BHT (Butylated Hydroxytoluene), resulting in a slight loss of ω-3 fatty acids.