The present study describes synthesis, characteristic and structural determination of different type of complexes formed in systems GeO2–H4Cit–X–phen–C2H5OH–H2O (where X is Cu(CH3COO)2, Cu(NO3)2, Zn(CH3COO)2, Zn(NO3)2, ZnCl2; H4Cit is citric acid; phen is 1,10-phenanthroline) depending on the anion of the initial 3d-metal salt. The complex compounds [Cu(phen)2Ge(Cit)2Cu(phen)2]·13H2O·C2H5OH·CH3OH (1), [Cu(H2O)(phen)2]2[{Ge(HCit)2}(NO3)2]·4H2O (2), [Zn(phen)3][Ge(HCit)2]·3H2O (3) were obtained for the first time. The compounds were characterized by elemental analysis, IR-spectroscopy, thermogravimetry. According to the single-crystal X-ray diffraction data, the structure 1 is trinuclear complex, while structures 2 and 3 belong to the cation-anionic type. Analysis of intermolecular interactions using Hirshfeld surface-based tools has indicated the dominant role of various contacts with participation of hydrogen atoms such as H…H, O…H/H…O, C…H/H…C for all compounds.