Graphene oxide (GO) is well known as an excellent amphiphilic material due to its oxygen-containing functional groups and its chemical tunability. By intercalation chemistry, organo-modified GO containing sulfonilic terminal groups were prepared and used as nanoadditive in Nafion polymer for the creation of hybrid exfoliated composites. The incorporation of hydrophilic 2D platelike layers in the Nafion membranes is expected to induce advantages in terms of thermal stability and mechanical and barrier properties (limitation of the methanol crossover by increased tortuosity and obstruction effect), although it may negatively affect the proton conductivity. In this work, we show how different preparation methods of the nanocomposites influence morphology, transport properties, and barrier effect to methanol. The hybrid membranes are characterized by powder X-ray diffraction and microscopies (SEM, TEM, and AFM). Water and methanol transport properties inside the nanocomposites are investigated by NMR spectroscopy (diffusivity and relaxation times), unveiling a reduction of the methanol diffusion and, nevertheless, an increase in the proton mobility and water retention at high temperatures. Finally, the electrochemical properties are investigated by direct methanol fuel cell (DMFC) tests, showing a significant reduction of the ohmic losses at high temperatures, extending in this way the operating range of a DMFC.