Soy beverage is a rich source of phytoestrogens isoflavones, with potential benefits on health. The effect of those compounds depends greatly on their bacterial metabolization into their aglycone forms. This study evaluated the health effects of two soy beverages, non-fermented (SB) and fermented with Bifidobacterium pseudocatenulatum INIA P815 (FSB), in acyclic and cyclic C57BL/6J aged female mice as a model of menopause and premenopause, respectively. SB and FSB treatments were administrated for 36 days and, subsequently, body weight, lipid and inflammatory profile and fertility were analyzed and compared. In addition, hepatic gene expression and faecal microbiota composition were also assessed. After fermentation, FSB presented a high content in the aglycones daidzein and genistein and a higher antioxidant activity. FSB treated cyclic mice showed a significant increase in the number of retrieved oocytes and zigotes. Differences in serum lipids were observed in triglycerides, which were lower in FSB than in SB groups. None of the treatments influenced the inflammatory profile or caused a dramatic change in the intestinal microbiota profile or hepatic gene expression in any of the groups. Our data showed that FSB provided greater health benefits than SB in lipid profile and fertility in cyclic mice. These beneficial effects could be attributed to the fermentation process, which produces more bioavailable and bioactive compounds, achieving a greater impact on health.