In the annals of human history, infectious diseases significantly influencing the collective well-being of people worldwide. Consequently, to identify effective agents for infectious ailments, the octahedral Co(II), Ni(II), Cu(II), Zn(II) complexes of 4-(3-methoxyphenyl)pyrimidin-2-amine and 2-methoxy-1-napthaldehyde based ligand were synthesized and well characterized in the current investigation. The synthesized compounds were evaluated for anti-TB, anti-inflammatory, antibacterial, antifungal activities by microplate Alamar blue, bovine serum albumin, serial dilution assays. The [Zn(L)(HO)] complex demonstrates robust potency with 0.0040 ± 0.0007 and 0.0038 μmol/ml MIC value in anti-tuberculosis and antimicrobial activities, correspondingly while 06.57 ± 0.03 μM IC value in anti-inflammatory investigation. Complex (5) show promising potential as targets for pathogen deformities, supported by rigorous biological and computational investigations including pharmacophore modelling, molecular docking (binding score -121.018 and -59.8662 kcal/mol for 6H53 and 1CX2 proteins, respectively), DFT (Density functional theory), MESP (Molecular Electrostatic Potential) and ADMET (absorption, distribution, metabolism, excretion and toxicity).