Fluorinated graphitic layers with good mechanical and chemical stability, polar C–F bonds, and tunable bandgap are attractive for a variety of applications. In this work, we investigated the photolysis of fluorinated graphites with interlayer embedded acetonitrile, which is the simplest representative of the acetonitrile-containing photosensitizing family. The samples were continuously illuminated in situ with high-brightness non-monochromatized synchrotron radiation. Changes in the compositions of the samples were monitored using X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The NEXAFS N K-edge spectra showed that acetonitrile dissociates to form HCN and N2 molecules after exposure to the white beam for 2 s, and the latter molecules completely disappear after exposure for 200 s. The original composition of fluorinated matrices CF0.3 and CF0.5 is changed to CF0.10 and GF0.17, respectively. The highly fluorinated layers lose fluorine atoms together with carbon neighbors, creating atomic vacancies. The edges of vacancies are terminated with the nitrogen atoms and form pyridinic and pyrrolic units. Our in situ studies show that the photolysis products of acetonitrile depend on the photon irradiation duration and composition of the initial CFx matrix. The obtained results evaluate the radiation damage of the acetonitrile-intercalated fluorinated graphites and the opportunities to synthesize nitrogen-doped graphene materials.