The impact that the structure of N-heterocyclic olefins (NHOs) has on the mechanism of action and efficiency in transesterification reactions as an organic catalyst is described for the first time. Two distinct mechanistic pathways, anionic and zwitterionic, have been separately investigated. The former is based on the formation of EtOH–NHO adducts and the latter on ester–NHO zwitterionic adducts. The thermodynamic stability of both types of adducts depends on the polarization degree of the olefinic bond of the catalyst. The thermodynamic stability of the ester–NHO zwitterionic adducts solely controls how efficiently NHOs behave in the zwitterionic pathway, which is the more favored one for all catalysts investigated, except for strongly twisted NHOs. The reaction rate along the anionic pathway is controlled by both the thermodynamic and kinetic stability of the EtOH–NHO adducts. Fully-planar imidazole-based NHOs perform the best along both pathways; however, those with bulky groups at the nitrogen atoms are preferred along the anionic pathway.