Enzyme-assisted aqueous extraction processing (EAEP) is an environmentally friendly process in which oil and protein can be simultaneously recovered from soybeans by using water and enzymes. The significant amount of protein-rich effluent (skim) constitutes a challenge to protein recovery. Countercurrent two-stage EAEP at a 1:6 solids-to-liquid ratio, 50°C, pH 9.0, and 120 rpm for 1 h was used to extract oil and protein from dehulled, flaked and extruded soybeans. Different enzyme use strategies were used to produce different skim fractions: 0.5% protease (wt/wt extruded flakes) in both extraction stages; 0.5% protease only in the 2nd extraction stage; and no enzyme in either stage. Dead-end, stirred-cell membrane filtration was evaluated with each skim. About 96, 89, and 66% of the protein were extracted with the three enzyme treatments, respectively. Protein retentate yields of 91, 96, and 99% were obtained for the three enzyme treatments, respectively, by using double membrane filtration (30 kDa/500 Da) of the skims, achieving permeate fluxes up to 1.24 kg/m 2 h at 3.9-4.8 concentration factors (CF) and 0.56 kg/m 2 h at 1.9-2.9 CF for 30 kDa ultrafiltration and 500 Da nanofiltration, respectively. For cross-flow ultrafiltration with the 3-kDa membrane, pH and presence of insoluble protein aggregates significantly affected permeate flux. Maximum permeate flux occurred at high pH and in the presence of protein aggregates, achieving a mean value of 4.1 kg/m 2 h at 1.7 bar transmembrane pressure.