The new poly-imidazole N8 ligand (S)-2-piperazinemethanamine-1,4-bis[2-((N-(1-acetoxy-3-(1-methyl-1H-imidazol-4-yl))-2-(S)-propyl)-(N-(1-methyl-1H-imidazol-2-ylmethyl)))ethyl]-N-(phenylmethyl)-N-(acetoxy), also named (S)-Pz-(C2-(HisIm))2 (L), containing three chiral (S) centers, was obtained by a multi-step synthesis and used to prepare dinuclear [Cu2(L)]4+ and trinuclear [Cu3(L)]6+ copper(II) complexes. Low-temperature EPR experiments performed on [Cu2(L)]4+ demonstrated that the two S = ½ centers behaved as independent paramagnetic units, while the EPR spectra used to study the trinuclear copper complex, [Cu3(L)]6+, were consistent with a weakly coupled three-spin ½ system. Theoretical models for the two complexes were obtained by DFT/RI-BP86/TZVP geometry optimization, where the structural and electronic characteristics nicely supported the EPR experimental findings. In addition, the theoretical analysis unveiled that the conformational flexibility encoded in both [Cu2(L)]4+ and [Cu3(L)]6+ arises not only from the presence of several σ-bonds and the bulky residues attached to the (S)-Pz-(C2-(HisIm))2 ligand scaffold, but also from the poor coordination ability of the tertiary amino groups located in the ligand side-chains containing the imidazole units towards the copper(II) ions. Both the dinuclear and trinuclear complexes are efficient catalysts in the stereoselective oxidation of several catechols and flavonoid compounds, yielding the corresponding quinones. The structural features of the substrate–catalyst adduct intermediates were assessed by searching the conformational space of the molecule through MMFF94/Monte Carlo (MMFF94/MC) methods. The conformational flexibility of the bound ligand in the complexes proves to be beneficial for substrate binding and recognition. For the dinuclear complex, chiral recognition of the optically active substrates derives from weak electrostatic interactions between bound substrates and folded regions of the ligand scaffold. For the trinuclear complex, in the case of L/D-Dopa, the chiral recognition has a remarkable stereoselectivity index of 75%, the highest so far reported for this type of reaction. Here the dominant contribution to stereoselectivity arises from the direct interaction between a donor group (the Dopa carboxylate) far from the substrate reaction site (the catechol ring) with the additional (third) copper center not involved in the oxidative catalysis. On the other hand, in the case of bulky substrates, such as L/D-catechin, the observed poor substrate recognition is associated with much weaker interactions between the chiral regions of the complex and the chiral part of the substrate.