Phosphate recovery from different second streams using electrodialysis (ED) is a promising step to a nutrients circular economy. However, the relatively low ED performance hinders the widespread adoption of this environmentally sound method. The formation of “bonded species” between phosphates and the weakly basic fixed groups (primary and secondary amines) of the anion exchange membrane can be the cause of decrease in current efficiency and increase in energy consumption. ED processing of NaxH(3−x)PO4 alkaline solutions and the use of intense current modes promote the formation of a bipolar junction from negatively charged bound species and positively charged fixed groups. This phenomenon causes a change in the shape of current–voltage curves, increase in resistance, and an enhancement in proton generation during long-term operation of anion-exchange membrane with weakly basic fixed groups. Shielding of primary and secondary amines with a modifier containing quaternary ammonium bases significantly improves ED performance in the recovery of phosphates from NaxH(3−x)PO4 solution with pH 4.5. Indeed, in the limiting and underlimiting current modes, 40% of phosphates are recovered 1.3 times faster, and energy consumption is reduced by 1.9 times in the case of the modified membrane compared to the pristine one. Studies were performed using a new commercial anion exchange membrane CJMA-2.