Given the growing popularity of incorporation of Lactobacillus acidophilus La‐5 in foodstuffs worldwide, we attempted to study the feasibility of probiotic jellies via microencapsulation technique. Three forms of jellies containing free bacteria, alginate beads and chitosan‐coated ones were developed and stored at different temperatures. The survival rate and gastrointestinal resistance of bacteria were investigated besides physical and organoleptic properties of jellies. Findings indicated that the encapsulated probiotics were protected against low pH and high temperatures with maximized sensory attributes despite the subsequent loss in turbidity. Moreover, chitosan‐coated microcapsules enhanced physical stability, spherical shape and metabolic activity in gastrointestinal system (GIS). The counts of coated L. acidophilus in the GIS could be maintained above 6 log10 CFU/g after 42‐day storage. In conclusion, microencapsulation with alginate, particularly when coated by chitosan, could successfully shield L. acidophilus against harsh processing and digestive conditions with desirable organoleptic and physical parameters. Practical Applications The fruity jelly desserts showed a remarkable potency as a food matrix to deliver Lactobacillus acidophilus so that they can pass through the gastrointestinal tract. Moreover, the incorporation of probiotic bacteria improved the organoleptic and physical properties of the final jelly product.