Epoxy (EP) coatings containing silica (SiO2) and (3-Aminopropyl)triethoxysilane-modified silica (SiO2-APTES) nanoparticles were prepared via the dip-coating technique on a zinc substrate. A detailed study was performed regarding their incorporation into the matrix, followed by the investigation of the newly obtained organic–inorganic hybrid coatings’ anti-corrosive properties. The two methods of embedding the nanoparticles were (I) modification of the silica nanoparticles with APTES followed by their introduction into the epoxy resin, and (II) functionalization of the silica nanoparticles in the epoxy gel before the addition of the hardener. It was observed that through the second method, the coating was homogeneous, with no sign of agglomerates. The nanoparticles were subjected to morpho-structural and physical–chemical analysis using Fourier-Transform Infrared Spectroscopy and Transmission Electron Microscopy, while the coatings were examined through Scanning Electron Microscopy and Energy-Dispersive X-Ray Spectroscopy, contact angle measurements and adhesion tests. The anti-corrosive performance of epoxy-coated zinc was analyzed using electrochemical impedance spectroscopy and polarization curves to investigate the impact of silanized SiO2 nanoparticle incorporation. Based on long-term corrosion testing, the epoxy-SiO2-APTES composite coatings showed a higher corrosion resistance than the undoped epoxy layer.