The high sensitivity of probiotic bacteria (PB) to many environmental factors limits the number of food products where they can be incorporated. This study aimed to examine the capability of a unique three-layered microcapsule structure to protect PB against extremely elevated temperatures and low pHs to allow their incorporation into bakery goods. The microcapsules were prepared first by granulation of a Bifidobacterium lactis (BL) strain, as a model PB, to form a core, and then coating the core with three consecutive protective layers. The physical features and the shape of the microcapsules obtained from three sequential preparations were characterized using various methods. A viable cell count was utilized to evaluate the efficiency of the microcapsule structure to protect the bacteria during a bread-baking process carried out at 180°C for 40min and also during the exposure to simulated gastric fluid (pH 1.2) for up to 1h. The results showed that whereas the free bacteria (unprotected BL) encountered a significant viability loss under these conditions, the microencapsulated BL presented superior resistance.