Nafion®/sulfonated-silica (NNS) membranes were prepared via the sol-gel reaction of 3-(trihydroxylsilyl)propane-1-sulfonic acid (THSPSA). The successful incorporation of silica was confirmed by Fourier transform infrared spectroscopy (FTIR). The feed concentration of THSPSA was found to have a significant effect on the in-situ formed silica structure and domain morphology. TEM results showed dense sulfonated silica nano-particles larger than the size of ionic clusters in Nafion matrix appearing in high THSPSA concentration (12 to 20 wt.%). The appearance of these dense silica nano-particles was accompanied by the changes in membrane properties. Ion exchange capacity (IEC), water uptake and proton conductivity showed similar trends as the THSPSA concentration increased, i.e. a significant increase from 0 wt.% to 12 wt.%, but only slight changes observed from 12 wt.% to 20 wt.%. A possible reason is that the sulfonic acid groups inside dense silica particles are not accessible and only surface sulfate groups have an effect on these properties. NNS membranes with 8 to 20 wt.% THSPSA loadings possess higher proton conductivity and lower methanol permeability compared with pristine Nafion® membrane, which indicates they are promising candidates for direct methanol fuel cell application. The decrease in methanol permeability could be due to the hindered pathway of methanol transport by dense silica nano-particles.