Current methods for the protection of metal surfaces utilize harsh chemical processes, such as organic paint or electro-plating, which are not environment-friendly and require extensive waste treatments. In this study, a two-step approach consisting of electrochemical assisted deposition (EAD) of an aqueous silane solution and a dip coating of a low surface energy silane for obtaining a superhydrophobic self-cleaning surface for the enhanced protection of copper substrate is presented. A porous and hierarchical micro-nanostructured silica basecoat (sol-gel) was first formed by EAD of a methyltriethoxysilane (MTES) precursor solution on a copper substrate. Then, a superhydrophobic top-coat (E-MTES/PFOTS) was prepared with 1H,1H,2H,2H-Perfluorooctyltriethoxysilane (PFOTS) for low surface energy. The superhydrophobic coating exhibited anti-stain properties against milk, cola, and oil, with contact angles of 151°, 151.5°, and 129°, respectively. The EAD deposition potential and duration were effective in controlling the microscopic morphology, surface roughness, and coating thickness. The E-MTES/PFOTS coatings exhibited chemical stability against acids, bases, and abrasion resistance by sandpaper. The proposed 2-layer coating system exhibited strong chemical bonding at the two interfaces and provided a brush-like surface morphology with long-lasting superhydrophobicity. The developed method would provide an environment-friendly and expedient process for uniform protective coatings on complex surfaces.