The objective of this study was to evaluate the stability of Bifidobacterium bifidum in the yoghurt with and without encapsulation. The B. bifidum was encapsulated with 6% sodium alginate concentration (SAC) and 0.8% Carboxymethyl‐Hexanoyl chitosan (CHC) as a single coating and then double‐coated with whey protein concentrate (WPC). After that, yoghurt was prepared with the addition of free and encapsulated probiotic (B. bifidum) along with the starter cultures and studied weekly up to 28th day of storage. Organoleptic analysis also shows higher score in encapsulated probiotic bacteria rather than free. The viable count of probiotic and yoghurt cultures was affected significantly (p < .01) during refrigerated storage of yoghurt and their survivability remained higher (8.81 ± 0.35 to 5.39 ± 0.58 log cfu/ml) in double‐coated encapsulated yoghurt. Encapsulated cells of probiotic culture have shown minimum zone of inhibition compared with free cells, and antibiotic (gentamicin) has shown maximum resistance against Salmonella. Practical applications The present study concludes that probiotics can be used against foodborne pathogens but antibiotic has shown more resistant as compared to probiotic. The most efficient and significant technology for probiotics preservation is encapsulation against unfavorable environmental conditions. So, to improve the physical stability of alginate gels, chitosan coating material enhanced the survival of encapsulated probiotic in the yoghurt. The results of this study can be used at industrial level to claim health benefits of encapsulated probiotics for consumers.