The potential of electrodialysis (ED) for the separation of amino acids (zwitterionic molecules that exhibit a specific charge behavior dependent on pH) has been demonstrated in the past. However, even though successful for the separation of specific amino acids, ED is not applicable for the separation of mixtures containing the positively charged amino acid arginine (Arg) due to its poisonous effect on commercially available cation exchange membranes (CEMs), while Arg is one of the major components in biobased feeds and an important precursor for the production of chemicals. The present study confirms that this inhibiting effect is directly related to the water content of the cation exchange membrane during the ED experiments. To overcome this limitation, ED with self-prepared cation exchange membranes with a high swelling degree (SPEEK) and ED with ultrafiltration membranes (EDUF) was applied. The results clearly prove that the separation of lysine (Lys) and Arg is possible with the two proposed alternative ED configurations. Separation of more complex biobased amino acid mixtures containing Arg showed the simultaneous separation of the acidic amino acids, glutamic acid (Glu) and aspartic acid (Asp), and the basic amino acids, Lys and Arg, from neutral alanine (Ala) validating the potential of ED for biorefinery applications.