This work investigates the characterization and performance of polyaniline and silica modified Nafion membranes. The aniline monomers are synthesized in situ to form a polyaniline film, whilst silica is embedded into the Nafion matrix by the polycondensation of tetraethylorthosilicate. The physicochemical properties are studied by means of X-ray diffraction and Fourier transform infrared techniques and show that the polyaniline layer is formed on the Nafion surface and improves the structural properties of Nafion in methanol solution. Nafion loses its crystallinity once exposed to water and ethanol, whilst the polyaniline modification allows crystallinity to be maintained under similar conditions. By contrast, the proton conductivities of polyaniline modified membranes are 3–5-fold lower than that of Nafion. On a positive note, methanol crossover is reduced by over two orders of magnitude, as verified by crossover limiting current analysis. The polyaniline modification allows the membrane to become less hydrophilic, which explains the lower proton conductivity. No major advantages are observed by embedding silica into the Nafion matrix. The performance of a membrane electrode assembly (MEA) using commercial catalysts and polyaniline modified membranes in a cell gives a peak power of 8mWcm−2 at 20°C with 2M methanol and air feeding. This performance correlates to half that of MEAs using Nafion, though the membrane modification leads to a robust material that may allow operation at high methanol concentration.