We studied the effect of chemical properties of substrates on the structural properties of perfluoropentacene (PFP) thin films grown by the supersonic molecular beam deposition technique. To this end, we have used m-carborane-1-thiol, template-stripped gold, and mica substrate surfaces and investigated the PFP film properties as a function of film thickness and molecular flux (deposition rate). On all three substrates, the PFP molecules adsorb in standing-up orientation in the first layer and overlayers. However, with an increasing hydrophobicity of the substrate, the mean grain size in the first layer increases. Bulk-like PFP films with needle-shaped grains grow on top of the first (wetting) layer on all the substrates, with smaller and taller grains on gold and larger and wider grains on mica surfaces.