Ion intercalation electrodes are being investigated for use in mixed capacitive deionization (CDI) and battery electrode deionization (BDI) systems because they can achieve selective ion removal and low energy deionization. To improve the thermodynamic energy efficiency (TEE) of these systems, flow-through electrodes were developed by coating porous carbon felt electrodes with a copper hexacyanoferrate composite mixture. The TEE for ion separation using flow-through electrodes was compared to a system using flow-by electrodes with the same materials. The flow-through BDI system increased the recoverable energy nearly threefold (0.009 kWh m−3, compared to a 0.003 kWh m−3), which increased the TEE from ~6% to 8% (NaCl concentration reduction from 50 mM to 42 mM; 10 A m−2, 50% water recovery, and 0.5 mL min−1). The TEE was further increased to 12% by decreasing the flow rate from 0.50 mL min−1 to 0.25 mL min−1. These findings suggest that under similar operational conditions and materials, flow-through battery electrodes could achieve better energy recovery and TEE for desalination than flow-by electrodes.