Microbial electrolysis cells (MECs) can effectively treat sulfate‐containing wastewater, but biocathode microorganisms, such as sulfate‐reducing bacteria (SRB), are susceptible to environmental influences. In practical wastewater treatment, the flow of water in the reactor generates shear forces that directly impact the growth and structure of the biofilm, which leads to changes in MEC efficacy. However, the sulfate reduction efficacy and biofilm community structure changes in MEC reactors under flow conditions have yet to be adequately evaluated. In this study, two‐chamber SRB biocathode MECs were constructed under flow conditions (experimental group [EG]) and stationary conditions (control group [CG]). The sulfate reduction rates of CG and EG were stable and reached 88.9% and 84.45%, respectively. The output voltage and current density of EG were similar to those of CG, indicating that the MEC could operate stably under flow conditions. The community structure of the biocathode indicated a high relative abundance of Desulfomicrobium from EG, which promoted the dissimilatory sulfate reduction pathway. This information reveals the potential of flow in improving the performance of MECs in treating sulfate‐containing wastewater.