Coating of ion exchange membranes used in electrodialysis with layers of polyelectrolytes is a proven approach that allows for the increasing of the limiting current, the suppressing of sedimentation, the controlling of the intensity of generation of H+ and OH− ions, and also the improving of monovalent selectivity. However, in the case when two materials with the opposite sign of the charge of fixed groups come in contact, a bipolar boundary is created that can cause undesirable changes in the membrane properties. In this work, we used a MK-40 heterogeneous membrane on the surface of which a layer of polyethyleneimine was applied by adsorption from a solution as a model of heterogeneous membranes modified with oppositely charged polyelectrolyte. It was found that, on one hand, the properties of modified membrane were beneficial for electrodialysis, its limiting current did not decrease and the membrane even acquired a barrier to non-selective electrolyte transport. At the same time, the generation of H+ and OH− ions of low intensity arose, even in underlimiting current modes. It was also shown that despite the presence of a layer of polyethyleneimine, the surface charge of the modified membrane remained negative, which we associate with low protonation of polyethyleneimine at neutral pH.