The alterations in current-voltage and transport characteristics of highly basic and strongly acidic ion-exchange membranes, during the electrodialysis of solutions containing a heterocyclic amino acid and a strong electrolyte, were studied. An increase in the catalytic activity of the water splitting process at the surface of heterogeneous MK-40 and MA-41 membranes upon prolonged contact with proline and tryptophan solutions was found. A significant effect of electroconvection on the components mass transfer through the cation-exchange membrane in the intensive current mode of electrodialysis was revealed for the solution containing a heterocyclic amino acid along with mineral salt (NaCl). This led to a reduction in the length of the “plateau” of the membrane’s current-voltage characteristics, in comparison with the characteristics for an individual sodium chloride solution with the same concentration. The changes in the characteristics of the studied ion-exchange membranes caused by contact with solutions containing heterocyclic amino acids during electrodialysis were reversible when applying electrochemical regeneration (cleaning in place) using the overlimiting current mode, corresponding to the region of facilitated transport for these ampholytes.