Probiotics are associated with health benefits to the host. However, their application can be limited due to a decrease in cell viability during processing, storage, and passage through the gastrointestinal tract. Microencapsulation is a simple and efficient alternative to improve the physical protection and stability of probiotics. The present study aimed to produce and characterize alginate or gelatin-based microparticles containing Lactobacillus acidophilus NRRL B-4495 or Lactiplantibacillus plantarum NRRL B-4496 by oil-in-water (O/W) emulsification and to evaluate the stability under storage conditions. The results showed that L. acidophilus and L. plantarum encapsulated in gelatin (LAEG and LPEG) presented diameters of 26.08 ± 1.74 μm and 21.56 ± 4.17 μm and encapsulation efficiencies of 89.6 ± 4.2% and 81.1 ± 9.7%, respectively. However, those encapsulated in alginate (LAEA and LPEA) showed an encapsulation efficiency of <1.0%. Furthermore, LAEG was stable for 120 days of storage at 5 °C and 25 °C. Therefore, encapsulation in gelatin by O/W emulsification is a promising strategy for protecting and stabilizing probiotic bacteria, enabling future application in foods.