The current research investigated and analyzed the influence of electrode surface enhancement on microbial fuel cell (MFC) efficiency under different flow circumstances. In this study, two double chamber cathode and anode, identically designed and built as a completely mixed system, were run for 60 minutes using yeast, salt, water, and sugar as anode substrate. The produced electrical current in MFC was determined for smooth and enhanced surface (punched plate) of a copper electrode in double chambers MFC for a range of stirring speeds 0, 250 rpm, and 500 rpm. The effect of air pumping and dispersion in each MFC chamber on the produced current was investigated under different stirring rates. A considerable electrical current was created due to the micro-organism bioactivity on the electrode surface, which caused a difference in the electrochemical potential between the two chambers. A remarkable increase in the produced current was noticed when the flow velocity was increased in the cathode chamber. However, the flow in the micro-organism chamber reduced the amount of the produced current. Enhancing the electrode surface by increasing the contact area with the biomass causes an increased mass transfer or charge transfer between the solution and the electrode surface. As a result of surface enhancement, an increase in the current output levels depends on the flow velocity. The conjoint effect of flow velocity and aeration, especially for the enhanced electrode surface, causes an appreciable increase of the produced current in MFC, reaching up to 3 times the smooth surface. The presence of air bubbles in the cathode chamber caused a noticeable increase in the produced current density. The presence of substrate glucose showed different influences on the produced current depending on the electrode surface.