The feasibility of recovering bioactive substances without surface activity from their aqueous solutions was studied using biosurfactants as collectors. For recovering the isoflavones from the soy whey wastewater, a two-stage batch foam fractionation was developed using the soy proteins as collectors. The results showed that when the conditions of the first stage were temperature of 60°C, pH of 5.0, volumetric air flow rate 80 of mL/min, and loading liquid volume of 400 mL, a high isoflavones enrichment ratio of 4.05 was obtained and the residual solution could be used as the feeding solution of the second stage. When the conditions of the second stage were temperature of 25°C, pH of 5.0, and volumetric air flow rate of 150 mL/ min, the soy proteins concentration in the residual solution could decrease to 622 mg/L. By reusing the foamate of the second stage as the feeding solution of the first stage, the total isoflavones recovery percentage reached 87.72%.