A simple and cost-efficient method to modify different surfaces in order to improve their bioactivity, corrosion and wear resistance proved to be sol-gel coatings. The silane layers have been shown to be effective in the protection of steel, aluminum or magnesium alloys and copper and copper alloys. Moreover, it has been found that the adding of different inorganic nanoparticles into silica films leads to increasing their performance regarding corrosion protection. In this study, we fabricated, a simple sol-gel method, transparent mono- and bi-layered hydrophobic coatings with simultaneous antibacterial, hydrophobic and anti-corrosive properties for the protection of metallic surfaces against the action of air pollutants or from biological attacks of pathogens. The first layer (the base) of the coating contains silver (Ag) or zinc oxide (ZnO) nanoparticles with an antibacterial effect. The second layer includes zinc oxide nanoparticles with flower-like morphology to increase the hydrophobicity of the coating and to improve corrosion-resistant properties. The second layer of the coating contains a fluorinated silica derivative, 1H,1H,2H,2H-perfluorooctyl triethoxysilane (PFOTES), which contributes to the hydrophobic properties of the final coating by means of its hydrophobic groups. The mono- and bi-layered coatings with micro/nano rough structures have been applied by brushing on various substrates, including metallic surfaces (copper, brass and mild steel) and glass (microscope slides). The as-prepared coatings showed improved hydrophobic properties (water CA > 90°) when compared with the untreated substrates while maintaining the transparent aspect. The corrosion resistance tests revealed significantly lower values of the corrosion rates recorded for all the protected metallic surfaces, with the lowest values being measured for the bi-layered coatings containing ZnO particles, both in the first and in the second layers of the coating. Considering the antibacterial activity, the most effective were the AOAg-II and AOZnO-II coatings, which exhibited the highest reduction of microbial growth.