The skim fraction (SF) obtained from enzyme‐assisted aqueous extraction (EAE) of soybeans is a by‐product with high protein content of up to 60.67%. As such, it is of great interest to develop an efficient method to recover protein from this fraction. In this study, the potential of dead‐end ultrafiltration (UF) in recovering skim protein extracted with different proteases was evaluated. Two polyethersulfone (PES) membranes with molecular weight cutoffs (MWCO) of 3 kDa and 5 kDa were utilized. Results revealed that the membrane with the MWCO of 5 kDa exhibited better filtration efficiency, since higher permeate flux values and lower impurity rejections were observed. Compared with Flavourzyme and Protex 7L, Alcalase 2.4L and Protex 6L exhibited stronger hydrolyzing ability, resulting in higher filtration fluxes but lower protein rejection coefficients. The recovered protein showed comparable amino acid profile to SPC, while with significantly reduced levels of trypsin inhibitors and phytate (p < 0.05), indicating high quality of the recovered protein. Overall, UF can be applicable to recover high value‐added protein from EAE of soybeans and remove undesired components from the resulting protein products.