The Mn-II-mediated transformation of 2-cyanopyrimidine to methylimidate in the presence of inorganic azide is proven through isolation and structural characterization of a metal complex. Though the reaction conditions are favorable for a "click" reaction leading to the formation of tetrazole, as evidenced from recent studies, we are astonished to see the formation of methylimidate in MeOH instead of tetrazole, which is supposed to form only in the presence of catalytic amount of corresponding alkoxide ion as base. The catalytic nature of this transformation reaction was confirmed by performing these experiments under catalytic conditions and analyzing the products using liquid chromatography-mass spectrometry techniques, which clearly showed similar to 96% and similar to 60% selectivity of methylimidate along with almost 100% conversion in the presence of Mn-II and Co-II as catalysts, respectively. In absence or presence of other metal ions like Cu-II, Ni-II, Fe-II, Zn-II, etc. only tetrazole formation takes place. So the present findings extended the formation of methylimidate catalyzed by metal ions in the presence of azide ion in alcoholic medium. Importantly, a probable mechanism for this unexpected transformation was framed based on the structural analysis and high-resolution mass spectrometry (electrospray ionization MS+) studies. The magnetic studies were also performed on complexes [Mn(L)(N-3)(2)](n) (1) and [Cu (L-2)(2)](n) (2a), showing anti-ferromagnetic character for compound 1 and negligible coupling for the copper complex 2a.