Amino acids from biobased feeds are an interesting feedstock for the production of biobased chemicals from cheap protein sources, as amino acids already have the required functionalities. Amino acids are zwitterionic molecules whose charge is determined by the surrounding pH. This makes the use of an electrical field as driving force for their separation, as in membrane electrodialysis (ED), attractive. Electrodialysis with commercially available ion exchange membranes was applied for the isolation of the basic amino acids L-lysine (Lys) and L-arginine (Arg) as a mixture and further separation of Arg from 1,5 pentanediamine (PDA), which is obtained from the enzymatic conversion of Lys. Electrodialysis experiments for the separation of PDA from Arg are carried out at three different pH values: 12.5 (PDA(0)/Arg(-0.5)), 10.9 (PDA(+0.5)/Arg(0)), and 10.0 (PDA(+1.5)/Arg(0)). Owing to the sensitivity of the charge of the amino acids with respect to pH changes, experiments at constant pH (using acid or base dosing or using a buffer in the feed solution) are carried out as well. Control of the pH significantly improves the performance of the process. The separation of PDA from Arg at pH = 10.0, when PDA has an average net charge of +1.5, resulted in the highest recovery (63%) at the highest current efficiency (83%) and significantly low energy consumption (3 kWh/kg). Depending on the conditions, pure streams of amino acids, either Arg (at pH = 12.5) or PDA (pH = 10.9) could be obtained, which shows the strength of the concept of enzymatic conversion combined with electrodialysis for the fractionation of amino acids for biorefinery applications.