Resource scarcity of petroleum products is driving the industry towards a bio-based economy. The feed streams for bio-chemicals, produced through fermentation of natural feedstocks are complex and viscous mixtures and often require a detoxification step to improve the growth conditions in the fermenter. This detoxification step could be performed by electrodialysis, a separation technology that is able to perform selective extractions of charged molecules with a high efficiency. The application of electrodialysis to these streams is heavily hampered by fouling from these bio-based streams. An improved stack design and optimisation of the operational parameters should increase the fouling resistance of these systems and mathematical modelling can accelerate this innovation process. A mechanistic model that includes fouling mechanisms can aid in understanding the fouling behaviour and can be used as a predictive tool for the innovation of stack design and antifouling procedures.