The reported work was focused on sol–gel-derived organically modified and fluorinated silica coatings deposited on elastic polymeric foil. The structure and topography of the coatings were tested by infrared spectroscopy and microscopic studies. The functional properties were determined using thermal analysis, surface analysis, and oxygen permeability tests. The barrier feature of the investigated materials against oxygen was correlated with the properties of the coatings. The hybrid (organic–inorganic) structure of the coatings was proven, demonstrating the presence of a silica network modified with alkyl and fluoroalkyl groups since precursors with the isooctyl group or different lengths of the fluoroalkyl chains were used for the syntheses. The coatings were free of defects and had a smooth surface except for the sample containing the longest fluoroalkyl chain (perfluorododecyl group), which showed a wrinkle-like surface. The hydrophobic character of the coatings increased, whereas the oxygen permeation coefficient values decreased (reaching a fourfold lower coefficient in comparison to the bare substrate) with a higher content of the fluorinated carbon atoms in the structure. The results were enriched by the information from the thermomechanical analysis as well as nanoindentation and scratch tests giving values of the glass transition temperature, thermal expansion coefficient, coatings adhesion, and hardness of the investigated systems.