Microbial fuel cells (MFCs) based sensors had been studied in measuring biochemical oxygen demand (BOD) or the equivalent chemical oxygen demand (COD) recently. Limited attention has been paid to the effect of the microbial communities in wastewater on the responses of these sensors. This study systematically evaluated, for the first time, the effect of wastewater samples from a variety of sources on the electrical response of a micro-fabricated double-chamber MFC device. It was found that the response of the MFC is positively correlated with the bacterial composition, in particular electroactive bacteria. The presence of aerobic bacteria in the sample reduces the current generation. These findings indicated that the bacterial content of the water sample could be a significant interference source and must be considered in the use of µMFC-based sensors. Filtering samples may be effective in improving the reliability of these microsensors.