The self-organization of functional proteins directly onto solid materials is attractive to a wide range of biomaterials and systems that need to accommodate a biological recognition element. In such systems, inorganic binding peptides may be an essential component due to their high affinity and selective binding features onto different types of solid surfaces. This study demonstrates a peptide-enabled self-assembly technique for designing well-defined protein arrays over a metal surface. To illustrate this concept, we designed a fusion protein that simultaneously displays a red fluorescence protein (DsRed-monomer), which is highly selective for copper ions, and a gold binding peptide AuBP. The peptide tag, AuBP, self-directs the organization of DsRed-monomer protein onto a gold surface and forms arrays built upon an efficient control of the organic/inorganic interface at the molecular level. The peptide-assisted design offers a modular approach for fabrication of fluorescent-based protein arrays with copper ion sensing ability.