In this study, inulin, whey protein concentrate (WPC 70) and skimmed milk powder (SMP) were used as nutritional factors to improve the quality of soy-drink fermented with indigenous Lactobacillus cultures. The growth behaviour (pH, titratable acidity, viable cell count), β-glucosidase, β-galactosidase, and proteolytic activity of indigenous Lactobacillus cultures were studied with various nutritional supplements in soy-drink. Two-way analysis of variance (ANOVA) was applied and the post-hoc comparison was acquired by Tukey’s HSD test for all the data presented in the study. Due to the supplementation of nutritional factors, the pH dropped as a bit of lactic acid production was also observed due to a lack of lactose. The supplements also provided extra nutrition during their growth in different incubation hours. At 2% rate of WPC 70 supplementation, maximum proteolysis (1.17 O.D.) was found by L. fermentum K7. L. fermentum K16 showed the highest β-glucosidase enzyme activity (0.154µM/mL/min) and maximum β-galactosidase activity (0.339 µM/mL/min) was observed for L. acidipiscis K27 at 2% rate of inulin supplementation to soy-drink. In the preparation of novel fermented foods and beverages, the conjunction of nutritional supplements with indigenous Lactobacillus cultures can potentially be used.