Establishing the rather complex correlation between structure and charge transfer in organicorganic heterostructures is of utmost importance for organic electronics and requires spatially resolved structural, chemical and electronic details. Insight in this issue is provided here by combining atomic force microscopy, Kelvin probe force microscopy, photoemission electron microscopy and low-energy electron microscopy for investigating a case study. We select the interface formed by pentacene (PEN), benchmark among the donor organic semiconductors, and a p-type dopant from the family of fluorinated fullerenes. As for Buckminsterfullerene (C60), the 2 growth of its fluorinated derivative C60F48 is influenced by thickness and crystallinity of the PEN buffer layer, but the behaviour is markedly different. We provide a microscopic description of the C60F48/PEN interface formation and analyse the consequences in the electronic properties of the final heterostructure. For just one single layer of PEN, a laterally complete but non-compact C60F48/PEN interface is created, importantly affecting the surface work function. Nonetheless, from the very beginning of the second layer formation, the presence of epitaxial and non-epitaxial PEN domains dramatically influences the growth dynamics and extremely well packed twodimensional C60F48 islands develop. Insightful element maps of the C60F48/PEN surface spatially resolve the non-uniform distribution of the dopant molecules, which leads to a heterogeneous work function landscape.