The overall objective of this work was to encapsulate L. casei ATCC 393 cells with PPI-alginate hydrogel capsules beads via extrusion. The effects of freeze-drying and subsequent storage at different temperatures on the viability of L. casei ATCC 393 cells were studied. Moreover, the capsules were tested in simulated gastrointestinal conditions just after their preparation and after a period of 84 days (12 weeks) of storage. The protective effect and the release profile of the capsules before and after storage were compared to examine their stability.