Hybrid organic–inorganic (O–I) nanocomposite coatings with an O–I matrix and inorganic nanofillers were synthesized by two consecutive and independent processes: sol–gel process (build-up of inorganic structures with epoxide-functions in situ) and polyaddition reaction (epoxy network formation with amines). Two O–I matrices were prepared: the GTMS–D400 type exhibits a high degree of regularity and self-ordering in the bulk (inorganic domains separated by elastic D400 chains) while in the GMDES–T403 type a linear inorganic polyepoxide is homogeneously mixed with the amino component without any separated inorganic domains. Inorganic nanofillers (natural or chemically modified montmorillonites and colloidal silica) differing in size and shape, were added to the matrices. Core properties of the composite products, on sub-micrometer and micrometer levels were studied by solid-state NMR spectroscopy, transmission electron microscopy, and wide-angle X-ray scattering. Macroscopic, bulk properties of the materials were investigated by static and dynamic mechanical analysis. The gas transport properties of the prepared coatings were tested with hydrogen and oxygen. The surface morphology of the coatings with and without nanofillers was determined by atomic force and scanning electron microscopy. A high degree of self-organization existing already in the O–I matrix was observed in some cases, which obviously influences the self-assembly behaviour of the nanofillers in the O–I matrix and on the surface of the hybrid coatings.