The energy contained in wastewaters has been identified as a promising sustainable energy resource that could be harvested by using microbial fuel cells (MFC). When dealing with real wastewaters, the MFCs should be able to manage high flow rates and flow rates fluctuations. In this work, the short-term effects of the influent flow rate variations on the performance of a microbial fuel cell has been studied. With this aim, the influent flow rate was stepwise increased from 0.72 to 7.2 L/d and then stepwise decreased. The obtained results indicate that, on the one hand, an increase in the influent flow rate leads to higher chemical oxygen demand removal rates up to 396 g/(L/d) and higher electric power generation almost 18 mW/m2, but to lower coulombic efficiencies. On the other hand, the reduction of the flow rate increases the coulombic efficiencies, as well as the percentage of chemical oxygen demand removed, but decreases electric power generation. In the short-term, the exposition to higher influent flow rates causes the growth of the microbial population of the MFC, the growth of the non-electrogenic microorganisms being higher than that of the electrogenic ones. The higher growth of non-electrogenic microorganisms may lead to lower coulombic efficiencies.