Development of microbial fuel cell (MFC) technology must address the challenges associated with energy extraction from large-scale MFC systems consisting of multiple modules. Herein, energy extraction is investigated with a 200-L MFC system (effective volume of 100 L for this study) treating actual municipal wastewater. A commercially available energy harvesting device (BQ 25504) is used successfully to convert 0.8–2.4 V from the MFCs to 5 V for charging ultracapacitors and running a DC motor. Four different types of serial connection containing different numbers of MFC modules are examined for energy extraction and conversion efficiency. The connection containing three rows of the MFCs has exhibited the best performance with the highest power output of ∼114 mW and the conversion efficiency of ∼80%. The weak performance of one-row MFCs negatively affects the overall performance of the connected MFCs in terms of both energy production and conversion. Those results indicate that an MFC system with balanced performance among individual modules will be critical to energy extraction. Future work will focus on application of the extracted energy to support MFC operation.