Organic proton-conducting molecules are presented as alternative materials to state-of-the-art polymers used as electrolytes in proton-exchanging membrane (PEM) fuel cells. Instead of influencing proton conductivity via the mobility offered by polymeric materials, the goal is to create organic molecules that control the proton-transport mechanism through supramolecular order. Therefore, a series of phosphonic acid-containing molecules possessing a carbon-rich hydrophobic core and a hydrophilic periphery was synthesized and characterized. Proton conductivity measurements as well as water uptake and crystallinity studies (powder and single-crystal X-ray analysis) were performed under various conditions. These experiments reveal that proton mobility is closely connected to crystallinity and strongly dependent on the supramolecular ordering of the compound. This study provides insights into the proton-conducting properties of this novel class of materials and the mechanisms responsible for proton transport.