This study was conducted to evaluate the viability and the physical properties of Bifidobacterium BB-12 microencapsulated by spray drying with partial replacement of reconstituted skim milk (RSM), as encapsulating agent, with the prebiotics inulin, oligofructose, and oligofructose-enriched inulin (at a ratio of 1:1, 200g L−1 total concentrations). The viable cell counts of the microcapsules were determined during storage for 180days at 4°C and at −18°C. The physical characterization included analysis of morphology, particle size, moisture content, water activity, dissolution, hygroscopicity, color, and thermal properties. All the microcapsules produced in this study showed a high survival rate of bifidobacteria during storage at the temperatures evaluated. The microcapsules produced with inulin and those produced with oligofructose-enriched inulin showed higher initial counts. However, blending oligofructose-enriched inulin with RSM and blending oligofructose with RSM resulted in better protection of bifidobacteria during storage. All microcapsules showed similar morphologies and particle sizes, between 14.45 and 18.78μm. The partial replacement with prebiotics decreased moisture content and water activity of the microcapsules. The time of dissolution in water was higher for the microcapsules produced with inulin, while the microcapsules produced with oligofructose were more hygroscopic. The value of a* increased in the microcapsules produced with prebiotics. The results of the thermal analysis suggest a higher stability of the microcapsules produced with prebiotics than those produced with RSM only.