Mixing plays a key role in both electricity generation and organic removal in microbial fuel cells (MFCs) via affecting substrate distribution and internal resistance. Herein, two mixing methods, anode electrode rotation and anolyte recirculation, were investigated in terms of energy consumption and production. Anode electrode rotation could increase the maximum power density and COD removal by 81.5 and 45.7%, respectively, when the rotating speed increased from 0 to 45 rpm. Likewise, anolyte recirculation also improved the power density and COD removal by 43.1 and 30.1%, respectively, at an increasing rate from 0 to 300 mL min−1. The enhancement of electricity generation became less significant at a high mixing level, likely because that substrate supply was relatively sufficient and other factors posed more effects on electricity generation. The MFC with anode electrode rotation achieved a higher energy balance (e.g., 0.254 kWh kg COD−1 at 35 rpm) than the one without any mixing (0.124 kWh kg COD−1), while anolyte recirculation led to a lower or even negative energy balance compared to that with no mixing. The results of this study have demonstrated energy advantages of anode electrode rotation and encouraged further exploration of energy-efficient mixing methods for MFC operation.