The surface‐enhanced Raman scattering spectra of 5 amphiphilic oligopeptides derived from EAK16 (AEAEAKAK)2, used as biomimetic coatings for medical devices, were obtained at 10−5–10−6 M in order to study the effects of systematic amino acid substitution along the peptide chain on the corresponding interaction with Ag colloidal nanoparticles. In addition, quantum‐mechanical data on 2 of the examined peptides were very useful for clarifying the assignment of bands, widely debated in the literature. In general, the peptide–nanoparticles interaction takes place through the COO− groups. The substitution of Ala by 2‐aminobutanoic acid in the sequence, corresponding to an increase of the hydrophobic chain length, is able to affect the peptide–Ag colloid interaction. It strengthens the interaction with NH3+ groups, mediated by the Cl− anions present in the colloidal solution, although the charge transfer interaction with the COO− ions remains the dominant interaction mechanism. When Tyr substitutes the hydrophobic Ala, the interaction mechanism is strongly affected because it takes mainly place through the Tyr residues, where the aromatic rings are predominantly perpendicular to the silver surface, partly as tyrosinate ion. Thus, the addition of the Arg‐Gly‐Asp sequence, useful to provide control on the bioactivity of the bone regeneration materials, does not change the interactions with the colloid, because the spacer amino acid substitution is the main factor affecting the peptide–nanoparticle interactions.