This study focuses on evaluating the efficiency of acid-tolerant Lacticaseibacillus paracasei bacteria encapsulated in an alginate-based gel matrix during repeated sourdough fermentation cycles, as well as their preservation during storage and throughout baking at high temperature. A double-coating procedure was applied, involving the encapsulation of bacterial cells in calcium alginate, which was further coated with chitosan. The encapsulation efficiency (EE) did not show significant difference between alginate and alginate-chitosan (97.97 and 96.71%, respectively). The higher number of L. paracasei bacteria was preserved in double-coated microbeads, with survivability rates of 89.51% and 96.90% in wet and dried microbeads, respectively. Encapsulated bacteria demonstrated effective fermentation ability, while double gel-coated cells exhibited slower acidification during sourdough fermentation, maintaining higher efficiency in the second fermentation cycle. The addition of freeze-dried, alginate-based gel-encapsulated bacteria (2-4%, w/w flour) significantly (p < 0.05) improved bread quality and extended its shelf life. A double-layer coating (alginate-chitosan) can be introduced as an innovative strategy for regulating the release of lactic acid bacteria and optimizing fermentation processes. Powdered alginate or alginate-chitosan gel-based L. paracasei microcapsules, at appropriate concentrations, can be used in the production of baked goods with acceptable quality and sensory properties, achieving a lactic acid bacteria count of approximately 106 CFU/g in the crumb, thereby meeting the standard criteria for probiotic bakery products.