Proton-Exchange Membrane Fuel Cells is a promising emission free energy technology. New generation of hybrid membrane for hydrogen fuel cells were produced from commercial sPEEK membranes, chemically and mechanically stabilized with a Sol-Gel (SG) phase. To study the process-structure-properties relationship of our alternative membranes we coupled Atomic Force Microscopy and Raman microspectroscopy on membranes prepared by cryo-ultramicrotomy without epoxy embedding. This paper demonstrates the powerfulness of co-localized AFM-Raman analysis, revealing the inner structure of hybrid membranes. We obtained quantitative data on the diffusion/condensation of SG precursors inside the sPEEK membrane. Co-localized analyses revealed the formation of skin layers with lower SG concentration on both sides of the membrane. The diffusion of species from the SG phase at the cross-section surface was observed at the first step of fabrication (insufficient SG condensation) and disappeared after hydrothermal treatments (improved SG condensation). The nano-mechanical data revealed a densification of the SG phase through the fabrication process. (C) 2018 Elsevier Ltd. All rights reserved.