In the present paper the distribution of phosphotungstic acid (PTA, H₃PW₁₂O₄₀) dispersed in sulfonated poly(ether ether ketone), SPEEK, was investigated by Anomalous Small Angle X-ray scattering (ASAXS) and Wide-Angle X-Ray Scattering WAXS techniques. The hydrolysis and condensation of 3-aminopropyltrimethoxysilane or zirconium tetrapropylate in this polymeric matrix were used to produce poly(3-aminopropyl silsesquioxane) or ZrO₂, as nanofillers. Contrary to previous results reported for membranes containing phosphomolybdic acid, the PTA could be completely dissolved in the SPEEK matrix. The applicability of the Guinier approximation for the SPEEK/PTA membrane confirmed that the PTA was dispersed as isolated nanoparticles. The incorporation of poly(3-aminopropyl silsesquioxane) in the SPEEK/PTA system caused the agglomeration of the heteropolyacid as 30 nm large particles. The ZrO₂ had little effect on the distribution of PTA in the SPEEK matrix. On the other hand, no crystallization of the heteropolyacid was observed in the membranes.