This study presented the encapsulation of an acidic sensitive probiotic strain L. casei ATCC 393 in PPI-alginate hydrogel capsules via extrusion technology. The matrix and the encapsulation process were considered compatible with the probiotic strain and showed an encapsulation yield of 85.69% ± 4.82. However, during the subsequent freeze-drying step, the capsules showed a lack of protection on the bacteria. The effects of freezing and dehydration on the viable cells in PPI-alginate hydrogels could be of interest in future studies. Incorporation of extra freeze-drying protectant (Santivarangkna et al., 2008) within the capsules could also be a target. During the storage test, the dried capsules displayed an excellent protection on L. casei cells at a storage temperature of 15 C. After freeze-drying and after 84 days of storage at 15 C, the capsules showed a weaker protective effect against acidic gastric conditions than fresh capsules but showed a similar release profile in SIF to fresh capsules. These results indicate that PPI-alginate hydrogel capsules may serve as carriers for the long term preservation of L. casei cells.