The reaction of diphosphoric acid (H4P2O7) with cobalt(II) chloride in the presence of 4-aminopyridine (4-AP) lead to a new Co(II)-diphosphate cluster based compound (C5H7N2)2[Co(H2P2O7)2(H2O)2]·2H2O (4APCoPPi). The novel material has been characterized by powder and single-crystal XRD methods, ICP and elemental analysis, IR, thermal analysis, UV–Vis and photoluminescence spectroscopy measurements. X-ray diffraction analysis reveal that the crystal building consists of monomeric [Co(H2O)2(H2P2O7)2]4− complexes based on corner-sharing CoO6 and H2P2O7 (PPi) polyhedra linked into a 3D hydrogen bonded framework featuring infinite 1D-channels extended along b-axis fully occupied by 4-AP cations. Furthermore, the optical studies of 4APCoPPi clearly visualized the six-coordinated distribution of the Co2+ ion and evaluated the band gap and the blue photoluminescence. Moreover, the complex was screened for antibacterial and anti-fungal activities against three strains showing excellent efficacy when compared to its basic reacting agents.