Among vegetable functional products, soy-based foods stand out for their high content in protein and flavonoids, mainly isoflavones. The fermentation of soy beverages with selected bacterial strains is a way to obtain a product enriched in isoflavone aglycones, alongside with other isoflavone derivates and other bioactive flavonoids. Two bacterial strains with high activity on the transformation of these compounds, Limosilactobacillus mucosae INIA P508 and Bifidobacterium pseudocatenulatum INIA P815, were tested for the fermentation of soy beverage. Both strains produced high concentration of the aglycones daidzein and genistein, in addition to a significant increase (P < 0.01) of glycitein, O-desmethylangolensin, 6″-hydroxy-O-desmethylangolensin, tetrahydrodaidzein and other flavonoid aglycones such as kaempferol, naringenin and luteolin. Two alternatives to conserve the developed functional beverages were explored, cold storage and thermal treatment. Refrigeration did not affect the concentration of isoflavones, even observing an increase in aglycones. Similarly, the thermal treatment and further room temperature storage did not reduce the amounts of daidzein and genistein. Therefore, both strains could be used for the development of soy beverages enriched in bioactive isoflavones and other bioactive flavonoids which would maintain their concentrations in refrigeration or at room temperature after heat treatment.