ABSTRACT Probiotic microorganisms are vital for gut health, but their viability is compromised by environmental stressors such as gastric acidity, bile salts, temperature, and oxygen. Encapsulation is a promising strategy to enhance probiotic stability and targeted release. In this study, Lacticaseibacillus rhamnosus and Lacticaseibacillus paracasei were encapsulated using an emulsion method with carob flour, a natural material with prebiotic potential. Encapsulation conditions were optimized using the Box–Behnken Design, considering mixing temperature, mixing time, and carob flour amount. The encapsulation efficiencies were 79.51% ± 0.36% for L. rhamnosus and 74.98% ± 0.20% for L. paracasei . Encapsulation induced significant compositional and structural changes, as confirmed by physicochemical, FTIR, and SEM analysis. Encapsulated probiotics exhibited higher viability than free bacteria during in vitro gastrointestinal digestion and under refrigerated and frozen storage. Encapsulation with carob flour is a promising approach to enhance probiotic stability and bioavailability in functional food applications.