Two probiotic strains were co-encapsulated in water in oil emulsion by two methods: (1) coaxial wet electrospraying and (2) freeze-drying methods. Optimization of the wet electrospray technique for maximum yield, minimum sphericity factor, and size resulted in an alginate concentration of 2.99% w/v, flow rates ratio of alginate to the emulsion of 4.81, and applied voltage of 10 kV. The cell viability of Lactobacillus plantarum PTCC 1896 was the same after both encapsulation techniques, while the freeze-drying method was more impressive (97.25%) than the coaxial electrospraying (86.46%) in maintaining the viability of Bifidobacterium animalis subsp. Lactis. Exposing electrospray-encapsulated probiotics to simulated gastrointestinal conditions for 4 h resulted in only a one logarithmic cycle decrease in the viability of both bacteria. The number of live cells remained at more than 108 CFU g−1. In contrast, the viability of freeze-dried probiotics was reduced to about 107 CFU g−1. The freeze-dried B. lactis was the most sensitive probiotic to simulated gastric conditions. Monitoring the viability of bacteria during storage at −18 °C for both wet electrospraying and freeze-drying methods showed that the number of living microorganisms was more than 6 Log CFU g−1 after 5 and 4 months, respectively.