The development of nanocarriers for drug/protein delivery is in focus today, as they can serve to both decrease dosages and improve localization to a desired biological compartment. A powerful tool to functionalize these carriers is specific affinity tagging supported by molecular recognition, a key principle in biology. However, the geometry of the binding region in a molecular recognition process, and thus its conformation and specificity, are in many cases poorly understood. Here, we demonstrate that short, model peptides, His(6)-tags, selectively recognize Cu(II)-trisnitrilotriacetic acid moieties (Cu(II)-trisNTA) when exposed at the surfaces of polymer vesicles designed to serve as nanocarriers or as surfaces for proteins binding. A mixture of poly(butadiene)-b-poly(ethylene oxide) (PB-b-PEO) and Cu(II)-trisNTA-functionalized PB-b-PEO diblock copolymers (10:1) self-assembles in aqueous solution, generating vesicles with a hydrodynamic radius of approximately 100 nm, as established by light scattering and TEM. Fluorescently labeled His(6) tags specifically bind to metal centers exposed on vesicles' surface, with a dissociation constant of 0.6 ± 0.2 μM, as determined by fluorescence correlation spectroscopy. The significant rearrangement in the geometry of the metal center upon peptide binding was characterized by a combination of CW-EPR, pulse-EPR, and DFT computations. Understanding the binding configuration around the metal center inside NTA pocket exposed at the surface of vesicles supports further development of efficient targetable nanocarriers that can be recognized selectively by molecular recognition in a biological environment and facilitates their immobilization on solid supports and their use in two-dimensional protein arrays.