Probiotics lose their viability during, formulation, processing, and storage. This work investigates the co-effect of three different combinations of encapsulation and prebiotics on the Survival of L. rhamnosus, L. acidophilus, and B. adolescentis under different conditions. In simulating gastric juice solution, the free cells survivability ranged between 36.5% to 40.5% for B. adolescentis and L. rhamnosus, after 2 hr, respectively. However, the encapsulated bacteria survival, ranged between 54.5% to 78.5% for B. adolescentis and L. rhamnosus, respectively. The encapsulated bacteria exhibited the highest survival rates, between 78.5%, and 76.5% for L. rhamnosus, and L. acidophilus, respectively, and 68.7% for B. adolescentis against the enzymatic gastric juice. In the simulating intestinal juice solution, cells encapsulated with resistant starch (ARs) and oligosaccharides (ARsG or ARsF) significantly enhanced survival over cells encapsulated with alginate alone and free cells, where the survivability was 104.4% for L. rhamnosus, 103.4% for L. acidophilus and 103.6% for B. adolescentis . A highly significant difference in survival rates was found between encapsulated and non-encapsulated bacteria when stored at 4oC and 25oC for 30 days. Survivability ranged between 31.5% to 77.1% was apparent for L. acidophilus and L. rhamnosus, respectively, after 30 days at 4oC. In contrast, free bacterial cells recorded a 29.1% to 31.5% survivability. After 30 days, the survivability of microencapsulated bacteria at 25oC ranged between 15.6% and 63.6%, while the survival rate of free bacteria declined between 10.9% and 13.5%. Overall, microencapsulation of the tested strains enhanced bacteria tolerance, survival, and storage periods, especially at 4oC.