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The aim of this work is the evaluation of a Sulfonated Poly Ether-Ether Ketone (S-PEEK) polymer modified by the addition of pure Santa Barbara Amorphous-15 (SBA-15, mesoporous silica) and SBA-15 previously impregnated with phosphotungstic acid (PWA) fillers (PWA/SBA-15) in order to prepare composite membranes as an alternative to conventional Nafion® membranes. This component is intended to be used as an electrolyte in electrochemical energy systems such as hydrogen and methanol Proton Exchange Membrane Fuel Cell (PEMFC) and Electrochemical Hydrogen Pumping (EHP). The common requirements for all the applications are high proton conductivity, thermomechanical stability, and fuel and oxidant impermeability. The morphology of the composite membranes was investigated by Scanning Electron Microscopy- Energy Dispersive X-ray Spectroscopy (SEM-EDS) analysis. Water Uptake (Wup), Ion Exchange Capacity (IEC), proton conductivity, methanol permeability and other physicochemical properties were evaluated. In PEMFC tests, the S-PEEK membrane with a 10 wt.% SBA-15 loading showed the highest performance. For EHP, the inclusion of inorganic materials led to a back-diffusion, limiting the compression capacity. Concerning methanol permeability, the lowest methanol crossover corresponded to the composites containing 5 wt.% and 10 wt.% SBA-15. [ABSTRACT FROM AUTHOR]