The present study aimed to improve the survivability of L. acidophilus encapsulated in alginate-whey protein isolate (AL-WPI) biocomposite under simulated gastric juice (SGJ) and simulated intestinal juice (SIJ). Microcapsules were prepared based on emulsification/internal gelation technique. Optimal compositions of AL and WPI and their ratio in the aqueous phase were evaluated based on minimizing mean diameter (MD) of the microcapsules and maximizing encapsulation efficiency (EE), survivability of cells under SGJ (Viability), and release of viable cells under SIJ (Release) using Box-Behnken experimental design. Optimal composition comprising 4.54% (w/v) AL, 10% (w/v) WPI, and 10% (v/v) AL-WPI gum in the aqueous phase was determined statistically. Physicochemical characteristics of the optimized matrix were investigated by SEM, FTIR, and XRD analysis to determine surface morphology, molecular bonds, and crystalline nature of such hydrocolloid. It could be concluded that the proposed biocomposite is a good promise for nutrients encapsulation in the food industry.