The detailed structure of F16CuPc films on SiO2 has been determined by means of in situ grazing incidence X-ray diffraction from the first monolayer to thicker films. In contrast to films of the homologous H16CuPc molecule, the F16CuPc films exhibit the same structure independently from the deposition temperature. The films show a thickness-dependent polymorphism manifested in the in-plane crystal structure, which implies large differences in the molecular tilt within the cofacial stacking of the molecules.