Microencapsulation is an up-and-coming technology for maintaining the viability of probiotics. However, the effect of core-to-wall ratios and ratios of polysaccharides on the protection of the Lactiplantibacillus plantarum 299v strain has not been deeply discussed. Lyophilization of the Lp. plantarum 299v strain was conducted, and different core-to-wall ratios and ratios of maltodextrin (MD) and resistant starch (RS) were applied. Results demonstrated that the content of MD and RS had an influence on the yield and bulk density in both core-to-wall ratios (1:1 and 1:1.5). In addition, samples coated with a core-to-wall ratio of 1:1.5 had significantly higher viability than those coated with a core-to-wall ratio of 1:1. Moreover, samples coated with core-to-wall ratios of 1:1 and MD:RS 1:1, as well as core-to-wall ratios of 1:1.5 and MD:RS 3:1, had the highest cell number after simulated gastric fluid and simulated intestinal fluid testing, respectively. Furthermore, the optimal formulation for the application of microencapsulated Lp. plantarum 299v in apple juice (serving as a functional beverage) is listed as follows: core-to-wall ratios of 1:1 and MD:RS 1:1, with the fortification method, and stored at 4 °C. After 11 weeks of storage, the cell count was 8.28 log (CFU/mL). This study provided a strategy for Lp. plantarum 299v to achieve high viability in long-term storage and provides an application in functional apple beverages.