By means of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS), we study and compare the crystalline and electronic structure of fluorinated and non-fluorinated pentacene fims on Cu(1 0 0). Pentacene perfluorination strongly affects its electronic structure both in the bulk and at the metal-organic interface. While the azimuthal anisotropy of the molecule-substrate interactions on Cu(1 0 0) remains unaffected by the fluorination, the interaction mechanisms, as concluded from their effect on the core-levels and on the conduction band of the respective molecules, show a completely disparate behaviour. (C) 2010 Elsevier B.V. All rights reserved.