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Abstract: pH-controlled separation of AAs was achieved by electro-membrane cell (EMC) with three compartments (central, comp. 1 and comp. 2). EMC is based on the principles of electrodialysis (ED) using indigenous cation-exchange and anion-exchange nanofilter (C-NF and A-NF, respectively). Water permeabilities (1.1–1.5mh−1 bar−1) and molecular cut-off (MWCO) values (400–500Da) for C-NF and A-NF, were suggested their nanofilter (NF) nature. Electrochemical properties of these membranes confirmed their suitability for EMC. Chronopotentiometric studies revealed the electro-transport of positively charged lysine (LYS+) and negatively charged glutamic acid (GLU−) across C-NF and A-NF, respectively, at pH: 6.1 under applied voltage. While glycine at its pI (pH: 6.1) remained immobile. Thus, separation of AAs (ternary mixture) by iso-electric point (pI) focusing of one component was proposed. Under optimized experimental conditions (i.e. at 4.0V constant applied voltage, pH: 6.1 for 0.05M equi-molar LYS–GLU–GLY mixture), about 4.0kWhkg−1 of AA separated energy consumption, 82% current efficiency and 90% product recovery showed the economic and technical feasibility of EMC for industrial exploitation. [Copyright &y& Elsevier]