This work presents the elaboration of porous silica nanospheres, eventually amine functionalized, which are used as the inorganic filler in mixed matrix silica/SPEEK membranes. The surface of the silica nanoparticles is modified by grafting (3-aminopropyl)dimethylethoxysilane (APDMS). The two sets of nanocomposite membranes obtained at varying silica loadings are characterized for their proton conductivity and water uptake properties. At higher degrees of sulfonation, some cross-linking due to the interaction of the amine groups of the silica with the sulfonic acid groups of the SPEEK polymer is attested by the water uptake reduction between the composites made with amine grafted or pristine silica particles. However, even in these conditions the proton conductivity of the mixed matrix membrane is not essentially different in the two sets of nanocomposites. This indicates that the inorganic filler effect on proton conductivity is related to changes in the microstructure of the water channels in the polymer lattice.