In this work, an integration of solid-liquid and liquid-liquid extractions by using aqueous micellar two-phase systems was evaluated as potential tool to purify soy isoflavones. Additionally, the proposed methodology aimed to preserve the protein content of the processed soy flour. The extractive assays were performed in AMTPS formed by Triton X-114 and sodium tartrate. In order to optimize the purification process, temperature and time were evaluated as independent variables. Under optimal working conditions, i.e. 100 min and 33 °C of incubation, IF were purified with a recovery percentage of 93 and a purification factor of almost 10. More importantly, the obtained sample presented an aglycone proportion superior to the reported by other methodologies. These results open perspectives to the use of aqueous micellar two-phase systems as an integrative methodology to extract, concentrate and purify isoflavones.