Probiotic strains must be able to withstand industrial manufacturing conditions and retain maximum viability and functionality during storage. Probiotic cells also have to survive the harsh mileu in the stomach and small intestine. Encapsulating probiotic cells with suitable agents helps them resist such adverse conditions and minimize the loss in viability. Four encapsulation materials were evaluated in the current study: Fructooligosaccharide (FOS), Maltodextrin (MD), Skimmed milk (SM) and Xanthan gum (XG). Cells were encapsulated using two commonly used techniques, spray drying (SD) and freeze drying (FD). Accelerated stability study on formulations was carried out as per ICH guidelines. Parameters like viability, water activity, residual moisture content, etc. were assessed to determine the shelf life. Viability losses in encapsulation by FD in the range of 4-27.5% were lower than by SD technique (the range of 19-40%). Approximately 60-80% of B. coagulans cells survived both SD and FD processing conditions, which is higher than 40-50% viability reported for Lactobacillus strains. Protective abilities of different encapsulation materials were in the order of: SM>FOS>MD>XG. Scanning electron microscopy of the encapsulated probiotics demonstrated that in the course of 90 days, surface of encapsulated particles developed some roughness, indicating their likely less stability.