Copper-fluoropolymer (Cu-CFx) nano-composite films are deposited by dual ion-beam sputtering. The extensive analytical characterization of these layers reveals that inorganic nanoparticles composed of Cu(II) species are evenly dispersed in a branched fluoropolymer matrix. In particular, X-ray photoelectron spectroscopy has been employed to study the surface chemical composition of the material and to assess how it changes on increasing the copper loading in the composite. Transmission electron microscopy reveals that the copper nanoclusters have a mean diameter of 2-3 nm and are homogeneously in-plane distributed in the composite films. Electrothermal atomic absorption spectroscopy has been used to study the kinetics of copper release in the solutions employed for the biological tests. The Cu-CFx layers are employed as bioactive coatings capable of inhibiting the growth of target microorganisms such as Saccharomyces cerevisiae, Escherichia coli, Staphylococcus aureus, and Lysteria. The results of the analytical characterization enable a strict correlation to be established among the chemical composition of the material surface, the concentration of copper dissolved in the microorganisms broths, and the bioactivity of the nano-structured layer.