Protective mechanisms of casein-based microcapsules containing mannitol on Lactobacillus acidophilus and Lactococcus lactis ssp. cremoris, changes in their secondary protein structures, and glass transition of the microcapsules were studied after spray-or freeze-drying and after 10 wk of storage in aluminum foil pouches containing different desiccants (NaOH, LiCl, or silica gel) at 25°C. An in situ Fourier transform infrared analysis was carried out to recognize any changes in fatty acids (FA) of bacterial cell envelopes, interaction between polar site of cell envelopes and microcapsules, and alteration of their secondary protein structures. Differential scanning calorimetry was used to determine glass transition of microcapsules based on glass transition temperature (T g ) values. Hierarchical cluster analysis based on functional groups of cell envelopes and secondary protein structures was also carried out to classify the microencapsulated bacteria due to the effects of spray-or freeze-drying and storage for 10 wk. The results showed that drying process did not affect FA and secondary protein structures of bacteria; however, those structures were affected during storage depending upon the type of desiccant used. Interaction between exterior of bacterial cell envelopes and microencapsulant occurred after spray-or freeze-drying; however, these structures were maintained after storage in foil pouch containing sodium hydroxide. Method of drying and type of desiccants influenced the level of similarities of microencapsulated bacteria. Desiccants and method of drying affected glass transition, yet no T g ≤25°C was detected. This study demonstrated that the changes in FA and secondary structures of the microencapsulated bacteria still occurred during storage at T g above room temperature, indicating that the glassy state did not completely prevent chemical activities.