In this study, the effects of various matrices consisting of maltodextrin and reconstitute skim milk and their binary and ternary mixtures with gum Arabic in the microencapsulation of Shirota by freeze-drying technique were assessed. Microcapsules produced with reconstitute skim milk showed high viability (>99%) after freeze drying. While the free cells were completely inactivated after exposure to simulated gastrointestinal conditions, the survival rates of microencapsulated Shirota were found high for all microcapsules except for maltodextrin and maltodextrin:gum Arabic formulas. The viability of microencapsulated Shirota during storage at refrigerate and room temperatures decreased between 0.39 and 2.43 log cycles and microcapsules produced with reconstitute skim milk:gum Arabic was found more durable at the both storage conditions. Reduction in the number of free cells was higher than encapsulated Shirota numbers during production of dessert, however the viability of encapsulated Shirota was found stable for 14 days of storage and consequently desserts containing encapsulated Shirota (except maltodextrin) showed stable pH values. This study revealed that combination of reconstitute skim milk:gum Arabic was an effective wall matrix for microencapsulation of Shirota by freeze drying and also very resistant against gastrointestinal fluids and storage conditions in view of protection of Shirota.