The highest encapsulation yields were obtained for the capsules made from PSY. Storage at 4 °C maintained the stability and viability of the organisms in the PSY capsules and offered better protection of viability than the other prebiotics after storage at the end of 30 days of storage. Lactobacillus plantarum (Lp33 and Lp17) were the bacteria that showed a higher viability during storage, maintained viability above the recommended minimum to offer their probiotic effect during storage. PSY and INU provided substantial protection to the Lactobacillus plantarum tested during simulated gastric and intestinal conditions above the recommended therapeutic minimum. The prebiotic addition in the probiotic bacteria encapsulation offers the possibility of adding the capsules inside different food products without affecting either the viability of the bacteria or their physicochemical characteristics.