A combination of computational methods based on molecular mechanics, fluorescence, FTIR and magic-angle spinning NMR spectroscopies, and thermogravimetric analysis coupled with mass spectrometry have been employed to explain the structure directing effect of dibenzyldimethylammonium (dbdm) and its bis(ortho- and meta-fluorobenzyl) derivatives in the synthesis of aluminophosphates with AFI-type structure. We identify a supramolecular assembly of dbdm cations with hydroxide anions which compensate for their positive charge. These hydroxide anions appear to be also coordinated to framework aluminum atoms, bridging the organic SDAs and the framework walls. Such assembly is most promoted when the fluorine atom is located in the ortho position of the aromatic ring, which considerably enhances the electrostatic interaction with the inorganic network. The presence of the OH− counterion provides charge balance for the ortho-fluorinated SDA and leads to fewer framework defects. In the other cases, most of the posit...