Aminophosphates are the focus of research on prebiotic phosphorylation chemistry. Their bifunctional nature also makes them a powerful class of organocatalysts. However, the structural chemistry and dynamics of proton-binding in phosphorylation and organocatalytic mechanisms are still not fully understood. Aminophosphine chalcogenides, preserving the H2N–P+–Ch− structural motif, represent well-suited molecular models that mimic proton-binding, hydrogen-bond switching and supramolecular self-assembling behavior of catalytically and prebiotically relevant molecules. Through spectroscopic (IR, 1H DOSY, 15N NMR), molecular dynamics, and computational investigations, the dynamic proton switching capability of aminophosphate analogs was demonstrated. It was shown under which conditions the amino (NH2) or chalcogen (Ch) functions in H2N–P+–Ch− structural units are protonated. In fact, all conceivable modes of hydrogen-bonding were identified, revealing substantial differences between the oxygen derivative and the heavier congeners. Using coordinating anions, supramolecular zigzag- and cube-shaped arrangements were found in the solid-state and in solution. After break-up of the cube structure, the sulfides and selenides no longer form stable interactions with HCl molecules. In the absence of coordinating anions, protonation of the chalcogen function is preferred. In contrast to the oxygen derivative, the heavier congeners show dynamic intramolecular proton-hopping between the chalcogen and the amino function.