Recently developed low fluorine containing polymers are advanced materials which confer advantageous properties to surfaces at a lower cost than conventional fluoropolymers (like PTFE), and are also more easily processable. Fluoropolymer surfaces are characterized by a low surface energy, high oleo and hydrophobicity, low coefficients of friction, among many other properties. This makes them desired materials in microelectronics, antifogging, antifouling and medical applications, to name a few. Fluorinated compounds are not easily coupled with macromolecules or common organic systems, and great efforts are made to compatibilize fluorinated species with hydrocarbon polymers. In this work, two chemical routes were explored in order to incorporate perfluorinated alkyl chains in an epoxy-amine based thermoset. On one side, a perfluoroalkyl thiolated molecule was used as a stabilizing ligand for silver nanoparticles, which were incorporated in the matrix polymer. On the other hand, fluorinated chains containing epoxy functionalities, were used as the matrix modifier. In the first case, fluorinated chains covering the nanoparticles, were mixed with the matrix, while in the second case, the fluoroalkyl chains were chemically linked to the network. Fluorine migration to the air—polymer interface was confirmed by X-Ray photoelectron spectroscopy (XPS). The materials hydrophobicity was then studied in terms of their contact angle with water (CA), as a function of the surface composition and the topography. Scanning electron microscopy (SEM) and atomic force microscopy (AFM), operated in moderate and light tapping modes, were used to morphologically describe the surfaces. An exhaustive surface analysis was made in order to explain the different hydrophobicity grades found.