The soy bean process water that is a by-product of soy processing technology can be utilized with a hybrid separation system recommended and investigated in this work. The aims of the soy bean water processing are to i.) concentrate the valuable components of the soy process water and ii.) reuse its water content. Two hybrid separation systems are considered and investigated: ultrafiltration followed by nanofiltration and centrifugal separation followed by nanofiltration. These hybrid separation systems are new in the area of their current application. Experiments verify that centrifugal separation is a more appropriate pre-treatment method for the removal of suspended solids and for the preservation of the sucrose content of the soy bean process water than ultrafiltration. Total sucrose can be rejected by nanofiltration membrane forming a sugar-rich retentate that contains other valuable components, too. Both tested hybrid processes result in clear and reusable permeates with low chemical oxygen demand that can be recycled to the production process reducing its water consumption and improving its sustainability. The recommended new hybrid separation system, centrifugal separation followed by nanofiltration, proves to be successful in this area of the biochemical industry.