BACKGROUND: Commercially lysine (Lys) is produced as lysine monohydrochloride (LysCl). The presence of chloride ion (Cl) in Lys makes it unfit for use in pharmaceutical and livestock feed industries. Various separation methods are required to achieve Lys from fermentation broths. This paper describes an electro-membrane reactor with three compartments (EMR-3) for the conversion of LysCl into Lys by in situ ion substitution and separation. RESULTS: The conversion of LysCl into Lys in EMR-3 is achieved by in situ ion substitution and separation using organic-inorganic hybrid anion-exchange membrane (AEM). It is found that the rate of Lys formation is dependent on applied current densities and LysCl concentration. The 96.2% Lys is recovered and low energy (2.07 kWh kg1) is consumed during the conversion of 0.10 mol L1 LysCl in EMR-3 at 10 mA cm2. Moreover, high current efficiency (93.02%) is achieved under the similar experimental conditions. CONCLUSIONS: On the basis of process parameters (high Lys recovery and CE and low W), it is concluded that the developed electro-membrane reactor can be efficiently applied for the conversion of LysCl into Lys in an economically viable manner. (c) 2012 Society of Chemical Industry