AbstractThe design of molecularly selective membranes is of paramount importance in the electrochemical separation of organic acids from complex fermentation streams, due to the presence of multicomponent species. However, current membrane‐integrated electrochemical technologies have relied on ion‐exchange membranes that lack intrinsic ion‐selectivity, thus preventing their application for value‐added recovery of organic acids from competing ions. Here, this study demonstrates a layer‐by‐layer polyelectrolyte functionalization approach for controlling ion‐selectivity, to achieve the multicomponent separation of organic acids in a redox‐flow electrodialysis platform. This study carries out a detailed investigation of the surface morphology and physicochemical properties of functionalized membranes, underlying that the selectivity of organic acids can be precisely tuned through the control of the hydrophilicity, electrostatic repulsion, and steric hindrance. Tailoring of membrane physiochemical properties enables up to complete retention of succinate, while enhancing the total flux. This organic acid retention is extended to the control over mono‐ and multivalent organic acids. Integration of functionalized membrane with the redox‐flow system allows selective succinic acid recovery with 99.7% purity from a synthetic fermentation mixture, high energy efficiency, and membrane stability. Modulation of ion‐selectivity through membrane functionalization coupled with electrochemical architecture design enables a sustainable pathway for multicomponent separations in biomanufacturing.