This study was aimed to prepare and characterize capsules loaded with Lacticaseibacillus rhamnosus GG (LGG), evaluating cell viability under gastrointestinal in vitro conditions and during storage in yogurt and apple juice, an alternative to traditional probiotic foods for people who are lactose intolerant. The capsules were prepared by ionic gelation, with an emulsification process as pretreatment. Cell viability of encapsulated LGG was evaluated after two different homogenization processes: magnetic stirring (AM) and Ultraturrax® homogenizer (UT). The system with the best relationship between viability and morphology was UT, which produced a viability of 85.80%. During in vitro evaluation, the capsules provided higher protection than free cells, up to 100% of cell viability. The morphology of capsules of both systems displayed a continuous and homogeneous surface. The cell viability of the encapsulated probiotics added in apple juice stored for 22 days at 4 °C was 86.16% for AM and 100% for UT, while the viability of free cells was 80.50%. In natural yogurt, the cell viability of the probiotics encapsulated stored 30 days at 4 °C was 100% for AM, 100% for UT, and 92.68% for free cells. This study suggests an alternative to preserve probiotic bacteria in a potential functional food