Microencapsulation and coating are preferred methods to increase the viability of the probiotic strains. The effect of microencapsulation technologies and materials used as microcapsule cores on viability is being investigated during development. In the present study, chitosan-coated and Eudragit L100-55-coated alginate microspheres were produced to encapsulate Lactobacillus plantarum probiotic bacteria. After the heat loading and simulated gastrointestinal juice dissolution study, the differences in viability were compared based on the CFU/mL values of the samples. The kinetics of the bacterial release and the ratio of the released live/dead cells of Lactobacillus plantarum were examined by flow cytometry. In all cases, we found that the CFU value for the chitosan-coated samples was virtually zero. The ratio of live/dead cells in the 120 min samples was significantly reduced to less than 20% for chitosan, while it was nearly 90% in the uncoated and Eudragit L100-55-coated samples. In the case of chitosan, based on some published MIC values and the amount of chitosan coating determined in the present study, we concluded the reason for our results. It was the first time to determine the amount of the released chitosan coat of the dried microcapsule, which reached the MIC value during the dissolution studies.