Microencapsulation is an efficient way to increase the survival rate of probiotics against harsh conditions. In this study, three probiotic strains (Lactiplantibacillus plantarum subsp. plantarum strain W2 (LP4), Lactiplantibacillus pentosus strain XL640 (LPE1), and Limosilactobacillus fermentum strain W8 (LF2)), isolated from shalgam and gilaburu, were microencapsulated with spray drying and process conditions [maltodextrin concentration (MC, 10–30%) and inlet air temperature (IAT, 110–130 °C)] were optimized by central composite rotatable design of response surface methodology. The results indicated that the predicted IAT and MC values for the maximum powder yield and viability were 123.21 °C and 22.76%, 130.37 °C and 19.49%, and 127.94 °C and 10.00% for LF2, LP4 and LPE1, respectively. At these conditions, bacterial viability ranged from 10.27 to 10.33 log colony-forming units per gram (cfu/g), while the powder yield values for the encapsulation of the bacteria were between 43.38% and 50.97%. Furthermore, MC was the most significant factor for the powder yield of LF2, LPE1, and viability of LPE1. Encapsulation efficiency values higher than 92.77% demonstrated the efficiency of spray drying for the protection of selected strains. The microcapsules produced at the optimum points had moisture content between 5.30 and 5.96%. SEM images showed that the microcapsules were in spherical shape. In conclusion, the results confirmed that the selected probiotics were successfully microencapsulated with spray drying with high powder yield, viability, and encapsulation efficiency levels and these features could reveal the potential of the encapsulated probiotic strains to be used in high-sugar foods.