Owing to the complexity of food matrices, process synthesis methodologies have not been as widely applied in the food industry as in the chemical industry. Here, we describe the application of a process synthesis methodology to design a system to separate valuable components from a byproduct of the soymilk production. The method yielded a number of potential processing pathways and relevant mechanistic questions, which required experimental input. The combination of considering the overall system on the level of general transformations, heuristics, and additional insights through experiments resulted in a simplified conceptual process design for the separation of isoflavones from okara with a globally more sustainable choice. The holistic approach within process design as an implication of the methodology is discussed.