Molecular crystals have been prepared from pentafluorophenylphosphonic acid (4). These include 2C6F5PO3H2·H2O (4·4·H2O), [(C6F5PO3H–)(H3O+)]·C6F5PO3H2 (4·4–·H3O+), [(C6F5PO3H–)(NH4+)]·C6F5PO3H2 (4·4–·NH4+), [(C6F5PO3H–)(Me2NH2+)] (4–·DMA+), [(C6F5PO3H–)(Me2NH2+)]·H2O (4–·DMA+·H2O), [(C6F5PO3H–)(Me2NH2+)]·C6F5PO3H2 (4·4–·DMA+), [(C6F5PO3H–)(Me2NH2+)0.5(NH4+)0.5] (4–·DMA+·NH4+), and [(C6F5PO3H–)(+H3NCH2CO2H)] (4–·Gly+), where DMA+ = dimethylammonium and Gly+ = glycinium. All of the assemblies incorporate an ammonium cation, a water molecule, or a hydronium ion in their structure, and these included species act as adhesive agents. They interact via O/N–H···O hydrogen bonds and C–H···O contacts with PO3H2 or PO3H– moieties located in polar sheets, forcing the building blocks to assemble with a 2D layered arrangement. The robustness of this arrangement is reminiscent of that observed in metal arylphosphonates and guanidinium sulfonates, yet the architectures described herein differ significantly from the second family of compounds in two aspects: the lack of puckering of the layers and the absence of void spaces to accommodate solvent molecules. Interestingly, however, just as in guanidinium sulfonates, two structural types have been recognized depending on the size of the included species: a single-layer stacking motif and a bilayer stacking motif. Even though hydrogen bonding is the prevailing interaction in these systems, the use of perfluoroaryl groups is also central, as these moieties bring about weak C–F···π, π···π, C–F···F–C, C–F···H–C, and O/N–H···F–C interactions that help to increase the cohesion of the nonpolar regions. As a result, new architectures are created that significantly differ in some cases from those prepared from phenylphosphonic acid. However, the weakness of perfluoroaryl-based interactions is also their strength, as these interactions are sufficiently flexible to allow changes in the organization of the aromatic groups in response to changes (ionization) occurring in the polar regions, as observed in the structures of 4·4·H2O and 4·4–·H3O+. This situation is quite unusual and may be regarded as some kind of acidity-modulated polymorphism. The work presented here broadens the knowledge on molecular crystal formation with arylphosphonic acids, a research area largely dominated by carboxylic and sulfonic acids. Also, the computational evaluation of 4·4·H2O and 4·4–·H3O+ described in this report suggests that this family of fluorinated compounds may show interesting prospects as molecular semiconductors, a research area that is currently receiving increased attention.