Diphosphonylated diazaheterocyclic compounds were synthesized in a one-step reaction by using dimethyl trimethylsilyl phosphite (DMPTMS) under acidic conditions. The reaction of DMPTMS with 1,5-naphthyridine yielded the corresponding diphosphonylated product through a tandem 1,4–1,2 addition under microwave conditions. This tandem 1,4–1,2 addition was also evaluated for other substrates, namely, 1,10-phenanthroline, 1,7-phenanthroline and 4,7-phenanthroline. Reactions under reflux and microwave conditions were compared. 1,5-Naphthyridine and the phenanthroline derived substrates are less reactive than previously investigated quinolines. The experimental trends in reactivity were rationalized by means of theoretical calculations. The intrinsic properties, such as aromaticity and proton affinities, showed distinct differences for the various substrates. Furthermore, the calculated free energies of activation for the rate-determining step of the tandem addition reaction enabled us to rationalize the differences in product yields. Both the theoretical and the experimental results show the substantial influence of the position of the nitrogen atoms in the (poly)aromatic compounds on the reaction outcome.