Establishing a better coordination between operating parameters and flow channel design is one of the most critical factors in achieving an optimum final performance of a fuel cell, since even a marginal change in any of the parameters can sharply affect the cell's performance. In this study, we report the use of three different acids, viz. sulphuric acid (H2SO4), formic acid (HCOOH) and phosphoric acid (H3PO4) as supporting electrolytes in combination with 2 M methanol fuel, wherein we demonstrated the effects of different combinations of acidic fuels and channel designs on the final cell performance. For this purpose, we made use of four different types of serpentine flow design. In the process, it was observed that an addition of 2 M concentrations of H2SO4 and H3PO4 enhanced the cell performance sharply in terms of current density, reaching values of 210 mAcm−2 and 180 mAcm−2, respectively, when analyzed at 0.2 V potential. This result was a considerable improvement over the current density value of 90 mAcm−2 achieved while using only 2 M methanol analyzed at the same potential. Moreover, the open-circuit voltage showed a value of greater than 0.6 V for both fuel samples. With a flow channel length of 650 mm (A5SF2) and at an open ratio of 52%, we obtained maximum power values of 42 mWcm−2 and 36 mWcm−2 for fuels containing 2 M H2SO4 (M2S2) and 2 M H3PO4 (M2P2), respectively, when analyzed at 70°C. Copyright © 2013 John Wiley & Sons, Ltd.