Modifying the surfaces of oxides using self-assembled monolayers offers an exciting possibility to tailor their surface properties for various applications ranging from organic electronics to bioelectronics applications. The simultaneous use of different molecules in particular can extend this approach because the surface properties can be tuned via the ratio of the chosen molecules. This requires the composition and quality of the monolayers to be controlled on an organic level, that is, on the nanoscale. In this paper, we present a method of modifying the surface and surface properties of silicon oxide by growing self-assembled monolayers comprising various compositions of two different molecules, (3-aminopropyl)-triethoxysilane and (3-glycidyloxypropyl)-trimethoxysilane, by means of in situ controlled gas-phase deposition. The properties of the resulting mixed molecular monolayers (e.g., effective thickness, hydrophobicity, and surface potential) exhibit a perfect linear dependence on the composition of the molecular layer. Finally, coating the mixed layer with poly(l-lysine) proves that the density of proteins can be controlled by the composition as well. This indicates that the method might be an ideal way to optimize inorganic surfaces for bioelectronics applications.