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The condensation product of 7-acetyl-6-azaindole and Girard’s T reagent ((E)-2-(2-(1-(1H-pyrrolo[2,3-c]pyridin-7-yl)ethylidene)hydrazineyl)- -N,N,N-trimethyl-2-oxoethan-1-aminium, HL ligand) was used as a ligand in the reaction with Cu(BF4)2·6H2O and NaN3. The reaction led to the formation of a binuclear Cu(II) complex containing two end-to-end (di-μ-1,3-N3) azide bridges, as well as two NNO-donor hydrazone ligands, forming an axially elongated square pyramidal geometry around each Cu(II) center. This end-to-end (di- μ-1,3-N3) azide bridge binding mode has not yet been reported, in Cu(II) complexes containing the NNO-donor hydrazone ligands, which makes the structure of the complex even more interesting for further studies. The complex was characterized by elemental analysis, IR spectroscopy and X-ray crystallography, and it was found that it crystallizes in the triclinic space group P–1 with the asymmetric unit comprising one Cu(II) centre, zwitterionic ligand L, one azide (N3 -) ligand and BF4 - counter anion. Examination of antimicrobial activity of the complex shows higher antifungal and antibacterial activity towards tested Gram-positive bacteria in comparison to the hydrazone ligand, with the antifungal activity of the complex even being comparable to the activity of amphotericin B.