Carbon paper has been widely used as a flow-through electrode to deliver the reactants through the electrodes in microfluidic fuel cells (MFCs). This electrode architecture can utilize the interior area in porous electrodes. Considering its disadvantages, such as a few functional groups, low specific surface area, and poor wetting property, it is necessary to actively treat the carbon paper. We study how the two activation methods, i.e., air annealing and acid oxidation, affect the contents of surface functionality, redox activity of iron ions, cathode resistance, and performance of MFCs. Our conclusion is that the two methods should be coupled together to achieve optimal surface physical and electrochemical properties: 303.23 +/- 3.09 mW cm(-3) in volumetric power density and 1541.75 +/- 134.17 mA cm(-3) in volumetric limiting current density, which are 1.57 and 1.75 times higher than that of a MFC with an untreated carbon paper cathode, respectively.