Estrogen receptor-positive (ER+) breast cancer is the most common cause of cancer death in women worldwide. Nowadays, the relationship between soya diet and breast cancer is controversial due to the unknown role of its isoflavones, genistein (G) and daidzein (D). In this work, we investigated not only the anti-tumor properties of a soybean extract (NBSE) but also whether the biotransformation of extract (BSE) by the fungus Aspergillus awamori increased its effectiveness. The BSE showed a stronger anti-aromatase activity and anti-proliferative efficacy in ER+ aromatase-overexpressing breast cancer cells. D and G were weak aromatase inhibitors, but inhibited cancer cell growth, being G the isoflavone that contributed to the BSE-induced effects. This work demonstrated that the biotransformation increased the anti-aromatase activity and the anti-tumoral efficacy of soybean extract in breast cancer cells. Moreover, it elucidated the potential use of soya in the prevention and/or treatment of ER+ breast cancer.