The thermal and structural stability of sulfonated cross-linked PEEK (polyether ether ketone) and its silicon-containing class II hybrid derivatives were characterized by combination of mass spectrometry, infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, and differential scanning calorimetry. Thermodynamic properties of the hybrids were determined, including glass-transition temperature, degree of crystallinity, and thermal stability. The decomposition processes of the hybrid polymers could be consistently interpreted and their energetics quantitatively determined. The introduction of inorganic silanol moieties improves the thermal stability compared to sulfonated products.