The Keggin-type polyoxometalate Li3PMo12O40 was evaluated for energy storage applications in non-aqueous media. In acetonitrile, using a static H-cell, high coulombic efficiency (∼90%) and stable (>500h) charge and discharge results were obtained. Different separators taking advantage of charge and size-based differentiation were compared for this system. Celgard®2325, Nafion®117 and aramid nanofiber-based membranes (ANF) were examined. Both Li-exchanged Nafion®117 and ANF membranes enabled stable charge/discharge cycles with high coulombic efficiency for this non-aqueous polyoxometalate system. The ANF membrane, which separates based on size, permitted operation at higher current densities than the Nafion®117 ion-exchange membrane.