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The viability of probiotics is strictly influenced by the production, storage, and digestion, while microencapsulation is a technology that can protect them against harsh environments. In this study, the impact of different core-to-wall ratios and wall material formulations on physical properties and the cell number of the microcapsules were investigated. The samples with core-to-wall ratio 1:1 have a significantly higher cell number, encapsulation efficiency, and bulk density than samples with core-to-wall ratio 1:1.5. The yields of the encapsulation method were changes in the opposite direction. Meanwhile, core-to-wall ratios and formulation have a significant effect on the cell number of the microcapsules during the in vitro SGJ test, whereas time, core-to-wall ratios, and formulation have a similar influence in the in vitro SIJ test. Moreover, probiotic apple juices stored at 4 °C for 6 weeks kept the highest cell number at the end. Furthermore, probiotic apple juices fortified by microcapsules coated with WP:DWP 1:1 in core-to-wall ratio 1:1 and stored at 4 °C for 4–8 weeks exhibited a significantly lower pH value. In summary, both whey proteins and denatured whey proteins are as good as coating material for microencapsulation of probiotic bacteria <i>Lactobacillus plantarum</i> 299v strains. These microcapsules have high potential in the production of probiotic apple juice even by fermentation or fortification methods.