Molecular self-assembly consists of the spontaneous aggregation of molecules into a well-defined structure guided by noncovalent bonds. The self-assembly strategy is ubiquitous in nature and recently has been proposed as a nature-mimetic strategy in polymer science and biomaterial engineering. In this context, we aim at designing and testing innovative but simple chemical strategies to efficiently modify surfaces by exploiting minor modifications in the bioactive molecule functionalities, for example, introducing cysteine (Cys) as a terminal residue in self-assembling peptides (SAPs). In this work, we report the attenuated total reflection-Fourier transform infrared spectroscopy, synchrotron radiation-induced X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, and time-of-flight secondary ion mass spectrometry investigation of self-assembled layers of oligopeptides anchored onto gold surfaces through cysteine residues, opportunely inserted in an SAP (EAK16-II) main chain in three different positions: at the amine end group, at the carboxyl end group, and at both terminal groups (i.e., a bidentate SAP). This study, which allowed us to individuate in the bidentate SAP the best candidate for the controlled production of ordered SAP layers on the gold substrate surface, is envisaged to open wide perspectives for efficient chemical modification of surfaces with biomolecules, leading to obtaining innovative bioactive materials for applications in the field of tissue engineering.