Synbiotics, which combine probiotics and prebiotics, represent an innovative approach to developing functional foods with enhanced health benefits compared to their individual components. This study focuses on the production of synbiotics through the microencapsulation of Lactobacillus strains isolated from traditional Mexican fermented beverages, contributing to the advancement of technologies for functional food development. Three Lactobacillus strains (Lacticaseibacillus rhamnosus LM07, Lactiplantibacillus plantarum LM19, and Levilactobacillus brevis LBH1070) were microencapsulated by spray-drying using a mixture of maltodextrin and gum arabic as wall materials and inulin as a prebiotic. The microencapsulation process achieved high survival rates (>90%), low moisture content (~5%), and low water activity (~0.3), ensuring long-term stability. Notably, the microencapsulated strains demonstrated improved tolerance to gastrointestinal conditions, enhanced adhesion properties, and increased antioxidant activity compared to non-microencapsulated strains. These results highlight the potential of microencapsulation as an innovative technology not only to preserve but also to enhance probiotic properties, facilitating the development of functional foods with improved health-promoting properties, extended shelf life, and stability at room temperature.