We present a comprehensive study of the complex interface between perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and the (111) surfaces of the three coinage metals. The specific structural, electronic, and chemical properties of the interface rendered by the different substrate reactivities are monitored with low-energy electron diffraction (LEED), x-ray standing waves (XSW), and ultraviolet and x-ray photelectron spectroscopy (UPS and XPS). In particular, the balance between molecule-substrate and molecule-molecule interactions is considered when interpreting the core-level spectra of the different interfaces. By presenting additional adsorption distances of the unsubstituted perylene, we showthat the molecular functionalization via end groups with acceptor character facilitates the charge transfer from the substrate but it is not directly responsible for the associated short adsorption distances, demonstrating that this frequently assumed correlation is not necessarily correct