We evidence the intercorrelation of electronic, structural, and morphological properties in nanorods of a substituted fluorine-based pentacene, 2,3,9,10-tetrafluoropentacene, deposited on gold single crystals by using photoemission and X-ray absorption spectroscopy investigations. Our investigations show changes in the XPS spectroscopy lines, and NEXAFS features correlate with the specific structure of the assemblies and their morphology. Consequently, the chemical structure affects not only the molecular electronic structure and the way the molecules assemble in a film but also the film morphology leading to specific thin film electronic properties.