The viability of Lactobacillus acidophilus and Lactobacillus reuteri combined or individually encapsulated in alginate (AG) or alginate-chitosan (AG-CH), when they were added to milk, peach nectar, or blackberry jam set-style yogurt; and stored at 5 °C for 30 days was evaluated. Survival of studied encapsulated lactobacilli when exposed to simulated gastrointestinal tract (GIT) conditions was also determined. AG-CH encapsulation provided better protection than AG and improved lactobacilli survival during storage in milk, peach nectar, or blackberry jam set-style yogurt; lactobacilli counts were ≥10 7 CFU/g after 30 days, except for encapsulated combined lactobacilli in peach nectar. Not significant (p < 0.05) changes in pH were observed when lactobacilli encapsulated in AG-CH were added to the evaluated foods. Minimal changes of pH were observed with lactobacilli encapsulated in AG (ΔpH < 0.49). During successive simulated GIT conditions, AG-CH encapsulation prevented lactobacilli loss in simulated gastric juices; meanwhile, favorable releases were observed in simulated intestinal fluids. Sensory evaluation demonstrated that judges did not perceive the presence of capsules in blackberry jam set-style yogurt, but were sensed in milk and peach nectar. Encapsulation of combined lactobacilli was successful and could provide more health benefits than individually encapsulated lactobacilli to consumers. Milk and blackberry jam set-style yogurt promoted microcapsules stability and thus viability of studied lactobacilli.