Probiotics confer numerous health benefits and functional foods prepared with these microbes own largest markets. However, their viability during transit from gastrointestinal tract is a concerning issue. Microencapsulation of probiotics is a novel technique of major interest to increase their survivability in GIT and food matrices by providing a physical barrier to protect them under harsh conditions. This article contributes the knowledge regarding microencapsulation by discussing probiotic foods, different methods and approaches of microencapsulation, coating materials, their release mechanisms at the target site, and interaction with probiotics, efficiency of encapsulated probiotics, their viability assessment methods, applications in food industry, and their future perspective. In our opinion, encapsulation has significantly got importance in the field of innovative probiotic enriched functional foods development to preserve their viability and long-term survival rate until product expiration date and their passage through gastro-intestinal tract. Previous review work has targeted some aspects of microencapsulation, this article highlights different methods of probiotics encapsulation and coating materials in relation with food matrices as well as challenges faced during applications: Gut microbiota; Lactic acid bacteria; Micro-encapsulation; Stability enhancement; Cell's release, Health benefits.