Configuration of BMED stack was improved to increase the recovery of citric acid. An acid recovery rate of 97.1% was reached with 3.3% sodium citrate at 40 mA cm−1. Pure base was obtained for reuse by filling mixed resins in base compartment. Voltage across acid compartment was greatly reduced by filling cation resins in it. BMED would be a promising technology to recover citric acid from fermented liquid.