Hydrogen technologies and especially fuel cells are key components in the battle to find alternate sources of energy to the highly polluting and economically constraining fossil fuels in an aim to preserve the environment. The present paper shows the synthesis of surface functionalized silica nanoparticles, which are used to prepare grafted silica/SPEEK nanocomposite membranes. The nanoparticles are grafted either with hexadecylsilyl or aminopropyldimethylsilyl moieties or both. The synthesized particles are analyzed using XRD, NMR, TEM, and DLS to collect information on the nature of the particles and the functional groups, on the particle sizes, and on the hydrophilic/hydrophobic character. The composite membranes prepared using the synthesized particles and two SPEEK polymers with sulfonation degrees of 69.4% and 85.0% are characterized for their proton conductivity and water uptake properties. The corresponding curves are very similar for the composites prepared with both polymers and the nanoparticles bearing the two functional groups. The composites prepared with the nanoparticles bearing solely the aminopropyldimethylsilyl moiety exhibit lower conductivity and water uptake, possibly due to higher interaction of the polymer sulfonic acid sites with the amine groups. The composites prepared with the nanoparticles bearing solely the hexadecylsilyl moiety were not further investigated because of very high particles segregation. A study of the proton conductivity as a function of temperature was performed on selected membranes and showed that nanocomposites made with nanoparticles bearing both functional moieties have a higher conductivity at higher temperatures.