The viability of encapsulated Lactobacillus acidophilus LA‐5 and Bifidobacterium bifidum BB‐12 by emulsion or extrusion techniques in Kasar cheese was investigated. The microbiological, biochemical and organoleptic properties of cheeses were assessed throughout 90‐day storage. Results showed that the viability of probiotic bacteria was maintained to a great extent by microencapsulation. No difference was noted between the two encapsulation techniques with regard to bacterial counts, proteolysis and organoleptical properties of the final products. Scalding caused a drastic decline in the counts of probiotic bacteria in all cheeses. Following scalding, while the numbers of nonencapsulated probiotic bacteria decreased continuously in the control cheese, the numbers of encapsulated bacteria remained well above the threshold for a minimum probiotic effect (107 cfu/g).