The microstructure of sulfonated poly(ether ether ketone) (sPEEK) membranes was investigated by combining small-angle neutron and X-ray scattering techniques (SANS and SAXS) for large and low water contents, respectively. The ion-exchange capacity, the water content and the nature of the counterion were varied for a better understanding of the membrane microstructure. SAXS and SANS contrast variation experiments reveal a significantly more complex structure than it is commonly believed with a delicate balance of the contrasts. At low water content, the structure can be depicted by the presence of small ionic clusters and larger more or less connected core-shell domains between crystallites for low values of the sulfonation degree. The first step of the swelling process corresponds to the filling without significant structural changes of the porosity created by the solvent evaporation during the casting process. The second step is associated with a major structural reorganization induced by a large increase of the membrane water content over a small range of temperature. This reorganization is attributed to an ionic domain percolation on a large scale. The third step corresponds to the swelling of lamellar ionic domains around the crystallites as revealed by the study of the dilution laws and of the structure of sPEEK ionomer dispersions. The sizes of the ribbon-like polymer particles were determined. They do not depend linearly with the membrane ion content suggesting a nonhomogeneous distribution of the ionic groups along the polymer chain during the sulfonation process associated with the semicrystalline nature of the polymers. Finally, the effect of the degradation in oxidative media on the membrane structure is shown to correspond to an increase of the membrane water content.