Proteins coated probiotic microcapsules can be applied to the apple juice to develop a functional probiotic beverage. 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 Lactobacillus plantarum 299v strains. These microcapsules have high potential in the production of probiotic apple juice even by fermentation or fortification methods.

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