While the connection between energy metabolism and biofilm growth control is well-established, this study seeks to expand on this relationship and demonstrate how it impacts both anodic biofilm and the performance of microbial fuel cells (MFCs) in the presence of proton exchange membrane (PEM) pollution. Through the use of chemical uncoupling agents DNP and TCS, the study inhibits biofilm synthesis to explore the role of growth control and metabolic changes in effectively managing PEM biological pollution and improving MFC performance. The findings of this study provide important insights into the mechanisms of biological fouling in PEM anode biofilms and contribute to the development of more effective cleaning strategies for preventing such biofilms.