The purpose of this work was to recover isoflavone aglycones from industrial soy whey wastewater, where the isoflavone aglycones mainly existed in the form of β-glycosides. First, foam fractionation was used for effectively concentrating the total soy isoflavones, including isoflavone aglycones and β-glycosides, from the wastewater. Fourier transform infrared spectroscopy indicated the existence of complexes of soy isoflavones and soy proteins. When soy proteins were used as the collectors, a high enrichment ratio of 3.68 was obtained under the optimal operating conditions of temperature of 50 °C, pH of 5.0, volumetric air flow rate of 100 mL/min, and loading liquid height of 400 mm. Subsequently, acidic hydrolysis was used for hydrolyzing β-glycosides in the foamate into aglycones. Using response surface methodology, a hydrolytic percentage could reach 96% under the optimum hydrolysis conditions of hydrolytic temperature of 80 °C, hydrochloric acid concentration of 1.37 mol/L, and hydrolytic time of 90 min.