The study aimed to develop innovative microencapsulated formulations of strains with probiotic attributes, Pichia kluyveri CCMA 0615 and Saccharomyces cerevisiae CCMA 0732. The yeasts (8 log CFU/mL) were microencapsulated by spray drying technique using whey powder (WP - 15 %, 20 %, and 30 %) and sodium alginate (ALG - 1 %). The microcapsules and cell viability were characterized during two months of storage (4 °C and 25 °C). The selected formulations were applied to functional beverage fermentation, and viability and survival in the simulated gastrointestinal tract (GIT) were performed. The viability of yeasts microencapsulated by the spray drying method was shown to be dependent on the strain and encapsulating matrix used, ranging from 84 to 99 %. P. kluyveri required refrigeration when storing microcapsules. In functional beverage fermentation, microencapsulated yeast maintained the same fermentative profile with carbohydrate consumption, production of lactic acid (0.30 to 1.10 g/L) and alcohol (0.2 to 1.61 g/L), and greater viability during storage. Finally, the microencapsulation of P. kluyveri with 15 % WP + 1 % ALG maintained high viability under GIT conditions, whether exposed independently (>84 %) or incorporated into a food matrix (>94 %). The study demonstrated that this innovative microencapsulation of probiotic yeasts increases their viability, improves biotechnological application, and facilitates efficient delivery of probiotics to the host.