Fermented soy foods are excellent sources of probiotics and can significantly enhance the nutritional profile of a diet. Our study aims to compare the physicochemical properties of soymilk fermented with five probiotic-type strains of Lactobacillus (Lb) and five newly isolated strains of Weissella (Ws). Soymilk fermented with novel Ws- and Lb-type strains at 12, 24, 36, and 48 hours of fermentation was used to study which strain is more effective in boosting the nutraceutical potential of fermented soymilk. Fermentation studies showed that soymilk fermented with novel strains of Ws- and Lb-type strains revealed an increased total antioxidant activity (2.21 times in Ws- and 2.14 times in Lb-fermented soymilk), decreased phytic acid (6.23 times in Lb; 4.12 times in Ws-fermented soymilk), and increased free mineral content for iron (5.38 in Lb; 3.16 times in Ws-fermented soymilk) and zinc (2.38 times in Lb; 3.96 times in Ws-fermented soymilk) compared to the unfermented soymilk. We also detected the hydrolysis of isoflavone glucoside into aglycones, i.e., an increase in daidzein, genistein, and glycitein (3.86/1.51-fold, 3.20/1.58-fold, and 3.31/1.55-fold for Lb and Ws, respectively), along with a decrease in hexanal (40.441-fold), and a rise in the viable count of bacteria. The novel strains of Weissella behaved similarly to the well-known Lactobacillus-type strains. A mixed fermentation method and further development of synbiotics in the future could use the two strains found in each group, Lactobacillus rhamnosus JCM1136 and Weissella confusa 30082b.