Potential probiotic strains, Lactobacillus delbrueckii subsp. lactis and Lactobacillus brevis were microencapsulated with their appropriate prebiotics, oat bran, and oats, respectively, selected by in vitro fermentation. The microencapsulation of these probiotics were done in an alginate matrix, with and without their appropriate prebiotics. Results showed that cells microencapsulated with the prebiotics had significantly more storage stability (p < 0.05) than free cells and cells microencapsulated without the prebiotics. The probiotic cells encapsulated with their appropriate prebiotic had improved survival rates when exposed to bile as compared to free cells. The survival of microencapsulated and free cells in the simulated gastric fluid and simulated intestinal fluid was also evaluated in this study. Microencapsulated probiotics, along with an appropriate prebiotic, were found to be more stable in bile, simulated gastric fluid and simulated intestinal fluid. Interestingly, this is the first work to use prebiotic such as oats and the oat bran to prepare the synbiotic microsphere.