The introduction of sulfonic acid modified silica in Nafion nanocomposite membranes is a good method of improving the Nafion performance at high temperature and low relative humidity. Sulfonic acid-modified silica is bifunctional, with silica phase expected to offer an improvement in membranes hydration while sulfonic groups enhance proton conductivity. However, as discussed in this paper, this may not always be the case. Proton conductivity enhancement of Nafion nanocomposite membranes is very dependent on silica particle size, sometimes depending on experimental conditions, and by surface modification. In this study, Sulfonated Preconcentrated Nafion Stober Silica composites (SPNSS) were prepared by modification of Stober silica particles with mercaptopropyltriethoxysilane, dispersing the particles into a preconcentrated solution of Nafion, then casting the membranes. The mercapto groups were oxidized to sulfonic acids by heating the membranes in 10 wt % hydrogen peroxide for 1 h. At 80 °C and 100% relative humidity, a 20%–30% enhancement of proton conductivity was only observed when sulfonic acid modified particle less than 50 nm in diameter were used. At 120 °C, and 100% humidity, proton conductivity increased by 22%–42% with sulfonated particles with small particles showing the greatest enhancement. At 120 °C and 50% humidity, the sulfonated particles are less efficient at keeping the membranes hydrated, and the composites underperform Nafion and silica-Nafion nanocomposite membranes.