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Longevity of probiotics is the main concern to confer positive health benefits to the host. Microencapsulation is one of the promising techniques to keep probiotics viable during storage and gastric transit. Immobilization can efficiently protect cells, making this technique potentially suitable for the industry for the delivery of probiotics to the gastrointestinal tract of humans through fermented dairy products. The objective of the study was to investigate the effect of single and double coating on the stability of Bifidobacterium bifidum in set type yoghurt. The encapsulation was carried out in two experimental plans. In the plan I, the B. bifidum was single coated with sodium alginate (SA) at 4%, 5%, and 6% and chitosan (CH) at 0.6%, 0.8%, and 1.0% concentrations. Based on their highest encapsulation efficiency (EE), single‐coated microbeads comprise of SA 6% and CH 0.8% were selected for double coating (plan II). Whey protein concentrate (WPC) at concentration of 5.0%, 7.5%, and 10% was used for double coating of SA 6% and CH 0.8% microbeads. The double‐coated beads with SA (6%), WPC (5%), and CH (0.8%) WPC (5%) further selected based on EE for yoghurt preparation. Different yoghurt treatments were prepared and stored (28 days) at 4 ± 2°C. All yoghurt samples were analyzed for physicochemical (pH, acidity), microbiological (viability of Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, B. bifidum), and sensory characteristics. It was noted that EE of double‐coated microbeads was greater than 90% as compared to single coated. It was also observed that pH decreases up to 4.2 and the acidity increased with the storage time. The count of probiotic and yoghurt cultures was affected significantly during storage but the survival rate of encapsulated treatments was maintained more than the minimum recommendation (107 CFU/ml) till the end of the storage period. The sensory properties of yoghurt containing double‐coated microbeads also significantly vary from the sample containing free cells of B. bifidum. It is concluded that double coating with the polysaccharides–protein matrix can maintain viability (>106 CFU/ml) for 28 days with no prominent change in physicochemical and sensory attributes as compared to free cells. The whey and its products (whey protein isolate and concentrate) can be recommended as a coating material for probiotics in future studies. Novelty impact statement: The research study investigates the effect and comparison of single and double coating with different coating materials on the viability of Bifidobacterium bifidum in set type yoghurt. In this study, dairy industrial waste, that is, whey has been used along with sodium alginate and chitosan in different combinations. [ABSTRACT FROM AUTHOR]