Phosphorylated heterocycles constitute an interesting class of molecules featuring complex, often unproven reaction mechanisms. Their synthesis is approached through experimental trial-and-error methods. Here we present a theoretical study of the reaction mechanism leading to the formation of thiazaphospholidine, as an example of such compounds. Our results reveal that proton rearrangement, rather than nucleophilic attack, plays a significant role in the rate-determining step of the reaction. This insight allows the prediction of which isomer will form from unsymmetrical reagents, potentially leading to more efficient experimental procedures for producing tailor-made structures that exhibit desired properties. We demonstrate that seemingly simple reactions, such as the nucleophilic substitution of an amino group on trivalent phosphorus, may require a more intricate explanation involving less favored tautomeric structures and a multi-step approach and are therefore not completely intuitive.