Three different types of copper(II) complexes have been studied of the hexadentate Schiff base ligand N,N′-bis[2-{(salicylidenimine)amino}ethyl] piperazine (H₂L) having the piperazine backbone in the chair form and axial–axial (a,a) N-atom lone pairs in the free state. The structure of the products is influenced by the reaction conditions and by the exogenous ligands, affecting the conformation of the piperazine moiety (primary structure) and the topology and nuclearity of the resulting complexes (secondary structure). In [Cu₂L(DMF)₂]X₂ (X = ClO₄⁻, 1a; NO₃⁻, 1b), the lone-pairs of chair-piperazine adopt the equatorial–equatorial (e,e) conformation. In the presence of NEt₃ and NaN₃, two types of [Cu^II₄] complexes [Cu₄(L)₂(OH)₂(H₂O)₂]X₂·nH₂O (X = ClO₄⁻, n = 1, 2a; X = NO₃⁻, n = 4, 2b) and [Cu₄(L)₂(N₃)₂(H₂O)₂]X₂·H₂O (X = ClO₄⁻, 3a; NO₃⁻, 3b) are obtained where four copper(II) ions are bridged by two hexadentate μ₃-piperazine ligands, this time in chair–e,a conformation, and by two OH and N₃groups. In CH₃CN, reactions of 1, 2 or 3 with NaN₃ always produce the double end-to-end azido bridged 1D polymer [Cu₂L(N₃)₂]_n (4) having a chair-e,e piperazine backbone. All studied conformations of the piperazine bridge mediate antiferromagnetic interactions between the Cu(II) ions, as revealed by bulk magnetization measurements. The striking difference in intensity of the coupling through trans-e,e piperazine observed for complexes 1a and 4 might be due to complementarily effects between the ligands involved.