We investigate the effect played by the presence of fluorine substituents in the organic molecules that act as structure directing agents during the synthesis of microporous materials, both in silica- and aluminophosphate-based compositions. We use a combination of experimental and computational approaches: first, experimental evidence is collected concerning the effect of fluorine on the structure directing ability; second, a computational study is performed with models of increasing complexity to explain the experimental results; third, whenever possible, experimental confirmation of atomic-level features emerging from the theoretical results is seeked. Different amines and ammonium ions with monofluorobenzyl groups are investigated; these aromatic molecules tend to associate through interaction of the phenyl rings, giving place to supramolecular arrangements that maximize the pore filling of the microporous structures. We have observed several effects caused by the presence of fluorine in the structure directing agents, depending on the type of molecule, the nature of the supramolecular arrangements, and the position of fluorine in the phenyl ring, which we classify into three types: (i) the presence of fluorine modifies the chemical character of the non-bonded interactions, increasing the electrostatic interactions with the microporous networks; (ii) fluorine can influence the ability to form supramolecular assemblies, required to direct efficiently the synthesis of the microporous structures; (iii) the presence of fluorine in certain positions of the aromatic rings can favour supramolecular assemblies of the organic molecules with other ions, such as fluoride or hydroxide anions, giving place to cooperative structure directing effects in the synthesis of microporous structures.