Recovery of water and soluble substances from soybean soaking water (SSW) was carried out using an integrated membrane system consisting of ultrafiltration (UF) and reverse osmosis (RO). It was found that even using the fourstage UF-UF-RO-RO process with pH adjustment, the quality of RO permeate did not satisfy the emission standard, while the RO permeate from the two-stage UF-RO treatment could be reused for soybean soaking. The chemical oxygen demand (COD) of RO permeate from this process was 1700-2800 mg/ L including acetic acid, γ-aminobutyric acid, lactic acid, alcohol, and other unidentified soybean extract with -C═O or -N-H groups, which had negligible effect on the subsequent soybean soaking. The RO permeate was reused for five cycles with addition of tap water (RO permeate/tap water=1:1.5), and the soaked soybeans were used for Koji making, which showed the similar properties with Koji made from soybeans soaked by tap water. Furthermore, the concentrates in the integrated UF-RO system provided a raw material for culturing algae or preparing animal feed. This work demonstrated that through UF-RO treatment, the wastewater pollution from food industry could be eliminated by resource recovery and utilization.