Fluorination is considered as a means of reducing the degradation of Fe/N/C, a highly active FeNx-doped disorganized carbon catalyst for the oxygen reduction reaction (ORR) in PEM fuel cells. Our recent experiments have, however, revealed that fluorination poisons the FeNx moiety of the Fe/N/C catalytic site, considerably reducing the activity of the resulting catalyst to that of carbon only doped with nitrogen. Using the density functional theory (DFT), we clarify in this work the mechanisms by which fluorine interacts with the catalyst. We studied 10 possible FeNx site configurations as well as 2 metal-free sites in the absence or presence of fluorine molecules and atoms. When the FeNx moiety is located on a single graphene layer accessible on both sides, we found that fluorine binds strongly to Fe but that two F atoms, one on each side of the FeNx plane, are necessary to completely inhibit the catalytic activity of the FeNx sites. When considering the more realistic model of a stack of graphene layers, only one F atom is needed to poison the FeNx moiety on the top layer since ORR hardly takes place between carbon layers. We also found that metal-free catalytic N-sites are immune to poisoning by fluorination, in accordance with our experiments. Finally, we explain how most of the catalytic activity can be recovered by heating to 900 °C after fluorination. This research helps to clarify the role of metallic sites compared to non-metallic ones upon the fluorination of FeNx-doped disorganized carbon catalysts.