Motivated by the possibility of modifying energy levels of a molecule without substantially changing its band gap, the impact of gradual fluorination on the optical and structural properties of zinc phthalocyanine (FnZnPc) thin films and the electronic characteristics of FnZnPc/C-60 (n = 0, 4, 8, 16) bilayer cells is investigated. UV-vis measurements reveal similar Q-and B-band absorption of FnZnPc thin films with n = 0, 4, 8, whereas for F16ZnPc a different absorption pattern is detected. A correlation between structure and electronic transport is deduced. For F4ZnPc/C-60 cells, the enhanced long range order supports fill factors of 55% and an increase of the short circuit current density by 18%, compared to ZnPc/C-60. As a parameter being sensitive to the organic/organic interface energetics, the open circuit voltage is analyzed. An enhancement of this quantity by 27% and 50% is detected for F4ZnPc- and F-8 ZnPc-based devices, respectively, and is attributed to an increase of the quasi-Fermi level splitting at the donor/acceptor interface. In contrast, for F16ZnPc/C-60 a decrease of the open circuit voltage is observed. Complementary photoelectron spectroscopy, external quantum efficiency, and photoluminescence measurements reveal a different working principle, which is ascribed to the particular energy level alignment at the interface of the photoactive materials.