Molecular electronics is an attractive option for low-cost devices because it involves highly uniform self-assembly of molecules with a variety of possible functional groups. However, the potential of molecular electronics can only be turned into practical applications if reliable contacts can be established without damaging the organic layer or contaminating its interfaces. Here, a method is described to prepare tightly packed carboxyl-terminated alkyl self-assembled monolayers (SAMs) that are covalently attached to silicon surfaces and to deposit thin metallic copper top contact electrodes without damage to this layer. This method is based on a two-step procedure for SAM preparation and the implementation of atomic layer deposition (ALD) using copper di-sec-butylacetamidinate [Cu(sBu-amd)](2). In situ and ex situ infrared spectroscopy (IRS), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and electrical measurements are used to characterize the chemical modification of the Si/SAM interface, the perturbation of the SAM layer itself, and the metal homogeneity and interaction with the SAM headgroups. This work shows that (i) carboxyl-terminated alkyl monolayers can be prepared with the same high density and quality as those achieved for less versatile methyl-terminated alkyl monolayers, as evidenced by electrical properties that are not dominated by interface defects; (ii) Cu is deposited with ALD, forming a bidentate complexation between the Cu and the COOH groups during the first half cycle of the ALD reaction; and (iii) the Si/SAM interface remains chemically intact after metal deposition. The nondamaging thin Cu film deposited by ALD protects the SAM layer, making it possible to deposit a thicker metal top contact leading ultimately to a controlled preparation of molecular electronic devices.