Electrodialysis (ED) has the potential to cost-effectively separate ions from organics in bio-refinery effluents, thereby simplifying downstream treatment and producing streams for possible valorisation. However, there is little information in the open literature regarding the impact of membrane selection for such systems. In this study, we have examined the effect of ion exchange membrane selection on key performance parameters (i.e. desalination rate, specific electrical energy consumption and the transfer of organics) using three commercially available anion and cation exchange membranes with bio-refinery effluents. It was found that the choice of anion exchange membrane had a significant impact, particularly after depletion of those anions having a high membrane permeability (e.g. chloride). The apparent stack resistance (and therefore the specific electrical energy consumption) was found to depend on the choice of anion exchange membrane (from 68 (1 for a PCSA/CMX membrane pair to 188 Omega for an AHA/CMX membrane pair with a cane molasses effluent); additionally the apparent stack resistance was also closely correlated with the amount of organics crossing the membrane. Collectively, these results show that careful membrane selection is critical, particularly when a high desalination rate is desired.