The total color difference of the microcapsules was not considered obvious to the human eye. The results of the thermoanalyses suggest an increase in the stability of the microcapsules produced with prebiotics. Finally, the results showed that the oligofructose-enriched inulin is the most appropriate prebiotic to be used as partial replacement of RSM to microencapsulate Bifidobacterium BB-12 by spray drying, with a great potential as a functional ingredient to be applied in dairy foods.