The discharge of excessive phosphorous into water bodies can lead to serious eutrophication threatening aquatic ecosystem. Membrane capacitive deionization (MCDI) is an effective platform for deionizing aqueous streams; however, conventional MCDI is unable to selectively remove targeted ions from a liquid mixture. In this work, we fabricated manganese oxide composite anion exchange membranes (AEMs) for MCDI to enhance phosphate removal selectivity from sodium chloride-sodium dihydrogen phosphate (10:1 molar ratio) aqueous mixtures. We systematically investigated several critical factors, such as constant current or voltage operation, applied voltage amount, process stream pH, and manganese oxide content in the AEM, on phosphate removal efficiency and phosphate selectivity. A trade-off was observed between phosphate removal and selectivity when increasing the cell voltage. Under the best conditions, an MCDI unit with a 20 wt% Mn2O3 composite AEM and a bipolar membrane facilitated high phosphate removal efficiency of ≥ 31.8 % and a phosphate over chloride selectivity of 1.1 while showing stability for at least 30 cycles. To help understand how manganese oxide particles boost AEM selectivity, static electronic structure calculations were performed, and they revelated that hydrogen phosphate absorption on Mn2O3 composite AEM was 314 kcal/mol more exothermic than that on pristine AEM while chloride adsorption on Mn2O3 composite AEM was 2.2 kcal/mol less exothermic than that on a pristine AEM. Overall, this work presents an effective strategy for selectively removing phosphate from model wastewater solutions and the mechanistic understanding that governs ion selectivity in composite ion-exchange membranes used in MCDI.