The study of protein adsorption at solid–liquid interfaces is a widely investigated research field because of its crucial relevance in biomaterial applications. In this article we provide detailed characterization of the interaction between two proteins, lysozyme and human serum albumin, characterized by different charge and structures, with two surfaces, gold or poly(methyl methacrylate), which differ in hydrophobicity and polarizability. The adsorption process has been performed by implementing experimental quartz crystal microbalance with dissipation monitoring and atomic force microscopy results with tuned molecular dynamics simulations. In this article, in fact, molecular dynamic simulations have been performed by considering several proteins in random orientations, approaching the surface from the solution. In this way, during the approaching process, not only protein interaction with the surface but also solvent molecules and the other proteins have been taken into account. Furthermore, to adequately simulate the surfaces, with regard to the gold surface, surface polarization and chemisorption have been taken into account, while a suitable new model has been proposed to describe the poly(methyl methacrylate) surface. The data obtained enable us to explain that the preferred interaction of the negatively charged human serum albumin protein with the gold surface (negatively charged) is mainly driven by chemisorption and polarizability, while the positively charged lysozyme preferentially adsorbs on poly(methyl methacrylate) because of both electrostatic and hydrophobic interactions. Interestingly, using this information, we have elucidated the challenging experimental results concerning the displacement of the two proteins on nanostructured surfaces made up of nanowell arrays.