In this paper, the feasibility of recovering the solvent from the aqueous ethanol solution of soybean isoflavones with nanofiltration (NF) was studied. Five commercially available polymeric NF membranes were employed and STARMEM 122 showed acceptable flux and high retention. The central composite design (CCD) of the response surface methodology (RSM) was applied to model the effects of temperature, pressure, and feed concentration on the permeate flux and the total soybean isoflavone retention. The results indicate that the developed models were in good agreement with the experimental results and they can be used to predict this NF process.