In the food industry, the microencapsulation process is important to control the release of active encapsulated ingredients, mask unwanted flavors, colors, and unpleasant smells, increase shelf life, and protect encapsulated components from light, moisture, and nutritional loss. In this process, microspheres are formed using cross-linked polymer, which can incorporate aqueous or oily ingredients, using simple physicochemical methods of phase separation by coacervation, without the need for organic solvents. In this context, this study aimed to develop bioactive, functional frozen yogurt through the incorporation of microspheres loaded with ascorbic acid or omega 3. The process used resulted in small microspheres (15-80μm), imperceptible to the palate, and capable of swelling about 14 times, being suitable for incorporating omega 3, without altering the swelling, and extending the shelf life of the ascorbic acid for 6weeks, even in an acid medium. Also, the matrix does not affect the properties of frozen yogurt and acts as a stabilizer, contributing to reduce the melting rate. The sensory analysis proved that encapsulation was promising to mask the taste and odor of omega 3 and to protect the ascorbic acid, without altering the properties and quality of the frozen product.