Equol and 5-hydroxy-equol, and their analogous compounds dehydroequol and 5-hydroxy-dehydroequol, are bioactive isoflavones formed by microbial metabolism. The aims of this work were to elucidate the formation of dehydroequol and 5-hydroxy-dehydroequol, to identify the role of dihydrodaidzein reductase (DHDR) in the production of equol, dehydroequol, 5-hydroxy-equol and 5-hydroxy-dehydroequol and to develop soy beverages enriched in these compounds through engineered lactic acid bacteria. DHDR was responsible for the production of equol and dehydroequol from dihydrodaidzein (DHD), and of 5-hydroxy-equol and 5-hydroxy-dehydroequol from dihydrogenistein (DHG), even in the absence of tetrahydrodaidzein reductase (THDR). The combination of DHDR with dihydrodaidzein racemase (DDRC), and/or THDR, allowed the production of soy beverages enriched in equol (241.34 ± 34.56 μM), dehydroequol (31.23 ± 5.78 μM), 5-hydroxy-equol (125.54 ± 7.90 μM) and 5-hydroxy-dehydroequol (292.34 ± 14.67 μM). Beverages fortified with high concentrations of equol, 5-hydroxy-dehydroequol and 5-hydroxy-equol could provide significant health benefits for consumers.