Flaxseed (Linum usitatissimum L.) is of interest as functional food because of the presence of compounds in its composition with potential health benefits, such as fatty acid omega-3, fiber, lignans and flavonoids. The bioactivity of lignans and flavonoids depends greatly on bacterial metabolism. Previously, lactobacilli and bifidobacteria strains were described to produce enterolignans and bioactive flavonoids (herbacetin, quercetin, quercetagetin, kaempferol, naringenin and eriodictyol) from flaxseed extracts and/or from secoisolariciresinol (SECO) in culture medium. In this work, cow's milk and soy beverage were supplemented with flaxseed extracts and fermented with selected lactobacilli and bifidobacteria strains. Lacticaseibacillus rhamnosus INIA P224, Limosilactobacillus mucosae INIA P508 and Lactiplantibacillus plantarum ESI 144 were capable of producing enterolactone (ENL) in both beverages supplemented with flaxseed, in addition to matairesinol and the flavonoids daidzein, genistein, glycitein, quercetin, naringenin, kaempferol and eriodictyol. On the other hand, Bifidobacterium breve INIA P367, Bifidobacterium pseudocatenulatum INIA P815 and Bifidobacterium pseudocatenulatum INIA P946 were able to produce quercetin, quercetagetin and high concentrations of herbacetin and SECO, in addition to pinoresinol, matairesinol, daidzein, genistein, naringenin, kaempferol and eriodictyol. The co-incubation of Lacticaseibacillus paracasei INIA P74 and Ligilactobacillus salivarius INIA P183 with Lactococcus lactis MG1363 harboring the food grade vector pLEB590.gly913, facilitated the production of ENL in soy beverage enriched with flaxseed. In this work, it is demonstrated how lactobacilli and bifidobacteria strains can improve the nutritional properties of flaxseed-enriched beverages, providing metabolites of great interest for human health.