The aim of the present study was to focus on the impact of two different methods and the effects of cryoprotectants on the survival of a probiotic bacterium, Streptococcus phocae PI80, during storage. For the protection of freeze dried cells, the optimal storage conditions were determined with a high survival rate. After the freeze drying process, all cryoprotectants exhibited a protective effect on cell viability at all storage temperatures. High relative cell viability was observed when cells were incubated at $-20^{circ}C$, which was optimum for the protection of S. phocae PI80. Trehalose was the most promising cryoprotectant at all temperatures during the storage period of bacterial cells. The combination of trehalose + skim milk showed more than 85% survivability compared to other combinations at $-20^{circ}C$ for 60 days. In addition, encapsulation of probiotic cells into alginate-chitosan gel capsules showed better survival of S. phocae cells ($5.468{pm}0.15$ LogCFU/mL) with high bacteriocin activity at $-20^{circ}C$ for six months. The cell-loaded microcapsules remained stable when treated with simulated gastric and intestinal fluids. After 6 h treatment, the capsules were found to be broken, releasing the probiotic cells directly into the intestinal system of rats. Therefore, microencapsulation was found to be the most efficient technique, which not only protected the cells for a longer time but also released the cells into the in vivo intestinal system.