Zwitterionic coordination compounds with strongly asymmetrical charge distribution were synthesized and characterized. Ring-substituted biimidazoles were used as the primary ligands for Zn and Cu compounds. Formation of Zwitterionic coordination compound was found to be strongly dependent on the pH of the reaction medium as well as on the ring and nitrogen substituents of the ligand. Reaction of the Df-R2biim (Df-R2biim = 2,2′-bi-1R-imidazole-5,5′-dicarboxaldehyde, R = Me, Et or Pr) with ZnCl2 in neutral conditions led to binuclear compounds [Zn2Cl4(Df-R2biim)2] with two bridging ligands (1a–c). Reaction with CuCl2·2H2O gave neutral mononuclear compound [CuCl2(Df-Me2biim)] (1d) with chelating biimidazole ligand. In acidic conditions (pH = 3–4) the imidazole nitrogens were either fully or partially protonated, which prevented the bidentate coordination of the ligands. Furthermore, aldehyde substituents of Df-R2biim ligands were involved in acetal formation with methanol solvent. Under acidic conditions the primary products were either ion pairs [MCl4][C14H24N4O4]·(M = Zn 3a, M = Cu 3b) with fully protonated H2L2+ counter cation or desired Zwitterionic coordination compounds [ZnCl3(C16H27N4O4)] (2a), [ZnCl3(C18H31N4O4)] (2b), [CuCl3(C16H27N4O4)] (2c), or [CuCl3(C18H31N4O4)] (2d) with partially protonated monodentate HL+ ligand. Zwitterions were obtained only with ligands having both aldehyde groups as ring-substituents and longer alkyl chains (ethyl or propyl) as N-substituents. In other cases ion pairs were formed as final products. Zwitterions were found to decompose in alcoholic solutions. In methanol solution, Zwitterionic compounds released neutral ligand and HZnCl3. All main products were characterized by NMR, elemental analysis and single-crystal X-ray diffraction.