The experimental electron density distributions (EDD) in tetrafluorophthalonitrile and tetrafluoroisophthalonitrile have been determined from a multipole refinement with use of accurate X-ray diffraction data collected at 100 K. As hydrogen atoms pose a serious challenge to a successful X-ray based EDD determination due to their diminishing diffraction power, the absence of any such atoms in the studied complexes is an important advantage. The experimental EDD is compared with theoretical densities resulting from high-level ab initio and DFT calculations using the atoms in molecules theory. Topological analysis of the electron density was used to compare the two different isomers and to estimate the similarity of identical functional groups in different crystalline environments. Comparison with theoretical results reveals subtle differences in C-F bonds. The experimental molecular electrostatic potential satisfactorily explains the observed differences in the patterns of weak intermolecular interactions.