The performance of a direct methanol fuel cell (DMFC) can be significantly reduced by methanol crossover. One method to reduce methanol crossover is to utilize a flowing electrolyte channel. This is known as a flowing electrolyte–direct methanol fuel cell (FE–DMFC). In this study, recommendations for the improvement of the flowing electrolyte channel design and operating conditions are made using previous modeling studies on the fluid dynamics in the porous domain of the flowing electrolyte channel and on the performance of a 1D isothermal FE-DMFC incorporating multiphase flow, in addition to modeling of the nonisothermal effects on the fluid dynamics of the FE-DMFC flowing electrolyte channel. The results of this study indicate that temperature difference between flowing electrolyte inflow and the fuel cell have negligible hydrodynamic implications, except that higher fuel-cell temperatures reduce pressure drop. Reducing porosity and increasing permeability is recommended, with a porosity of around 0.4 and a porous-material microstructure typical dimension around 60–70 μm being potentially suitable values for achieving these goals.