The presented work aimed to investigate the dependence of the fluoroalkyl precursors, used in the sol–gel synthesis of silica-based materials, on the structural and optical properties of the final coating deposited on polyethylene terephthalate foil. The structural properties of the fabricated coatings were analyzed using Raman Spectroscopy, X-ray Photoelectron Spectroscopy, and Scanning Electron Microscopy with Energy Dispersive Spectroscopy (SEM-EDS). The morphology of the samples was investigated using SEM and Atomic Force Microscopy methods. Optical properties were analyzed using ellipsometry and reflectometry. Additionally, the wettability properties with the surface free energy were determined. The cracks-free layers were obtained on the elastic substrate as proved by microscopic observations. The expected chemical structure was confirmed using spectroscopic studies that showed fluoroalkyl chains build into the final structure. The coatings (except the one obtained from the precursor with the longest fluoroalkyl chain) exhibited smooth surfaces and high transparency with a transmittance of 92% in the visible range. They had low refractive indices, which could be tuned in a wide range from 1.435 down to 1.347 (at 633 nm) by changing the fluorinated precursors and increasing the amount of fluorine in the material. A longer fluoroalkyl chain also improved the hydrophobic character of the coating. Such materials have great potential application in flexible photonic structures (for example in photovoltaics). Highlights, Influence of fluoroalkyl chains on structural, morphological, and optical properties of silica-based coatings on flexible substrate . • Fluorinated silica-based hybrid coatings deposited on polymeric foil were reported • The structural properties of the fabricated coatings were analyzed • The wettability properties with the surface free energy and optical properties were determined • The modification of properties depending on the content of fluorinated carbons was shown