Stability of enzymes such as β-galactosidase (β-gal), β-glucosidase (β-glu), lactate dehydrogenase (LDH), pyruvate kinase (PK), hexokinase (HK), and ATPase of microencapsulated Bifidobacterium animalis ssp. lactis Bb12 after freeze-drying and after 10 wk of storage at low water activity (aw) at room temperature was studied. Bacteria were microencapsulated using alginate formulation with or without mannitol fortification (sodium alginate and mannitol [SAM] and sodium alginate [SA], respectively) by creating gel beads followed by freeze drying. Two types of dried gel beads were then stored at low aw, such as 0.07, 0.1, and 0.2; storage in an aluminum foil was used as control. All storage was carried out at room temperature of 25 ◦C for 10 wk. Measurement of β-gal, β-glu, LDH, PK, HK, and ATPase (with or without exposure to pH 2.0 for 2 h) activities was carried out before freeze drying, after freeze drying, and after 10 wk of storage. There was a significant decrease in almost all enzyme activities, except that of PK. SAM and SA showed no different effect on maintaining enzyme activities during freeze drying. Storage for 10 wk at room temperature at various low aw using SAM and SA system had a significant effect on retention of most enzymes studied, except that of PK and LDH. Storage at aw of 0.07 and 0.1 was more effective in maintaining enzyme activities than storage at aw of 0.2 and in an aluminum foil. However, mannitol fortification into alginate system did not significantly improve retention of enzymes during 10 wk of storage.