Redox flow batteries (RFBs) based on aqueous organic electrolytes are a promising technology for safe and cost-effective large-scale electrical energy storage. Membrane separators are a key component in RFBs, allowing fast conduction of charge-carrier ions but minimizing the cross-over of redox-active species. Here, we report the molecular engineering of amidoxime-functionalized polymers of intrinsic microporosity (AO-PIMs) by tuning their polymer chain topology and pore architecture to optimize membrane ion transport selectivity. AO-PIM membranes are integrated with three emerging aqueous organic flow battery chemistries, and the synergetic integration of ion-selective membranes with molecular engineered organic molecules in neutral-pH electrolytes leads to significantly enhanced cycling stability.