Hybrid alginate-soy protein isolate-based hydrogel beads were prepared and evaluated to enhance the survival of the encapsulated probiotics (Lactobacillus plantarum) during heat processing to incorporate in mango juice. The solutions of sodium alginate-soy protein isolate (SA-SPI) with probiotic cells were dropped into the gelation bath containing calcium chloride (3% w/v) solution to develop various types of hydrogel beads. The level of survival of probiotics in encapsulated beads under acidic conditions (pH 2, 3, and 6.5) and bile salt (0.5 and 1.0% w/v) was evaluated. The survival of the encapsulated probiotics to thermal processing was evaluated by treating the beads in saline solution (0.9% w/v) at 30, 50, 63, and 72°C. The encapsulated probiotic bacteria were found alive even after treatment at 72°C for 90 s. Most of the free cells did not survive at the temperature higher than 50°C and very low pH (pH 2 and 3). The survival of probiotic cells was found higher with the hybrid hydrogel beads containing alginate and soy protein isolate (1:8 w/w). Furthermore, mango juice fortified with encapsulated L. plantarum in hydrogel beads was subjected to thermal pasteurization at 72°C for 90 s.