An increase of isoflavone aglycone content in soy foods can be attained through fermentation with food-grade bacteria. In this study, two commercial soy beverages with distinctive chemical composition (AS and VS) were fermented by strains of lactobacilli (eight strains) and bifidobacteria (two strains) with high β-glucosidase activity. Along fermentation, growth of the strains and isoflavone deglycosylation in the soy beverages were monitored. Large differences in growth, aglycone content and chemical parameters in AS and VS beverages fermented by different species and strains were observed. Isoflavone glycosides were completely transformed into their corresponding aglycones by most strains during fermentation of AS beverage, whereas large amounts of undeglycosilated isoflavones were still present in fermented VS. Four strains showing strong deglycosylation activity and appropriate technological properties (Lactobacillus casei LP71, Lactobacillus plantarum E112, Lactobacillus rhamnosus E41 and Bifidobacterium pseudocatenulatum C35) were proposed as industrial starters to improve functionality in soy-based fermented foods.