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In the present work, complexes of cobalt(II), copper(II), and zinc(II), 2-amino-4-methylpyrimidineand, and 2,3-diaminopyridine were successfully prepared and characterized using elemental analysis, UV-visible, and FTIR spectroscopy, as well as magnetic susceptibility measurements, molar conductance, TGA analysis, and X-ray diffraction. From elemental and spectral data, the formulae [M(L1)(L2)Cl2(H2O)] (where L1 = AMPY (2-amino-4-methylpyrimidine) and L2 = DAPY(2,3-diaminopyridine)) and M = Co(II) (2), Cu(II) (2), and Zn(II)) for the metal complexes have been proposed. The geometric structures of the mixed-ligand complexes were found to be octahedral around the metal ions, and the XRD patterns showed monoclinic crystal systems with space group P21. The mode of bonding was pentacoordinate for Cu and hexacoordinate for Zn and Co. Different features may result from the fact that not all molecules have the same electron distribution. For example, Zn and Co have larger electron densities in at least one of the chlorides in the HOMO compared with pentacoordinate Cu, which has a small electron distribution on the chloride. Thermal analysis indicated that all metal complexes are stable up to about 88 °C with thermodynamically favored overlapped chemical reactions. Excellent antibacterial and antifungal activity was shown by the three synthesized forms of the complexes. The Zn(II) complex had a high level of antioxidant activity with a DPPH scavenging of 91.5%, whereas the Cu(II) complex had a low level of antioxidant potential (16.5%). The docking tests also showed that all compounds had good binding energy levels (7.2–7.9 kcal mol−1). For this reason, all molecules can easily fit in the receptor protein’s catalytic sites. However, the Co(II) complex is shown to be more active.