The objectives of this study were to encapsulate the Bifidobacterium bifidum F-35 into whey protein for the production of one-layer microcapsules, and then the microcapsules were covered by sodium alginate to produce double-layer microcapsules for examining the effectiveness of microcapsules in set yogurt. The reinforced treatment by double layer exhibited a significant increase (P < 0.05) in B. bifidum F-35 count more than the treatments of free cells and one-layer microcapsules. Microcapsules of double layer in yogurt led to record a value of titratable acidity that was 1.51 in comparison with the treatments of one layer and free cells that were 1.65 and 1.73, respectively. The hardness values were recorded as 206.88 at the treatment of double layer and 130.31 at the treatment of one layer after 7 days of storage. Microencapsulation of double layer caused a slight bitterness and creamy texture in yogurt, whereas the samples of free cells were described to have sour and bad texture.