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Whey protein isolate is a suitable carrier system for probiotics in addition to sustained and targeted release in gastrointestinal tract. In this study two different wall materials namely, whey protein isolate with sodium alginate and denatured whey protein isolate with sodium alginate were employed for microencapsulation of Lactobacillus plantarum (mtcc 5422) using spray drying and freeze drying techniques. Microencapsulated powders final moisture content, cell survival (before and after drying), particle morphology and stability in simulated acidic and bile conditions were investigated. It was observed that the moisture content of the spray dried powder was lower than freeze dried powder and spray drying method produced almost 9–12% less cell survival compared to freeze drying method. In simulated acidic and bile conditions denatured whey protein encapsulated cells showed better stability than undenatured whey protein. This study indicated that combination of denatured whey protein isolate and sodium alginate wall matrix was able to deliver probiotics with improved survival rate and suitable for controlled core release applications.