To investigate the protective effects of various wall materials on probiotics, two types of Lactiplantibacillus plantarum 90 (Lp90) microcapsules were prepared using sodium alginate and chitosan (Lp-AC), soy protein isolate (SPI) and reducing sugars conjugate (Lp -MRP) as wall materials, respectively. The physical properties, cell viability under different conditions and the application of the microcapsules were investigated. Results showed that the selected wall materials were safe to Lp90 and their simulated digestion products exhibited antioxidant activities and prebiotic properties. The encapsulation efficiencies of Lp-AC and Lp-MRP were above 80%. Both microcapsules significantly enhanced cell survival rates under various conditions including low pH, bile salts, thermal processing, mechanical force, storage, and gastrointestinal digestion, with Lp-MRP demonstrating superior protective effects. When incorporated into milk and orange juice and stored at 4°C for 28 d, the colony counts of beverages containing Lp90 microcapsules exceeded 6 Log CFU/mL, with minimal changes in total soluble solids. Lp-MRP exhibited higher cell viability and smaller viscosity changes at 25°C for 28 d. Therefore, the single-layer encapsulation using SPI and reducing sugars conjugate showed promise over traditional chitosan-alginate double-layer encapsulation concerning probiotic protection, targeted delivery, and application.