This research article provides a comprehensive analysis of the preparation, structural characterization, 3D modeling, and biological screening of two novel formulated metal complexes, NiPDBZNPH and CuPDBZNPH. These complexes were obtained by combining 2,2′‐pyridine‐2,6‐diylbis(1H‐benzimidazole) (PDBZ) and 2‐hydroxy‐naphthaldehyde Schiff‐base (NPH) ligands with Ni(II) and Cu(II) ions, resulting in the compounds [Ni (NPH)(PDBZ)(Cl)] and [Cu (NPH)(PDBZ)(Cl)], respectively. Spectroscopic and analytical techniques confirmed that both complexes exhibit octahedral geometry around the central metal ion. Computational studies using density functional theory (DFT) corroborated the molecular structures and investigated the quantum chemical properties of the ligands and complexes. A series of in vitro assays were conducted to assess their anti‐inflammatory, antifungal, antibacterial, and antioxidant properties, revealing enhanced bioactivity compared to the uncoordinated ligands. The potential of NiPDBZNPH and CuPDBZNPH as therapeutic candidates was also explored through interactions with calf thymus DNA (CT‐DNA). Molecular docking simulations targeting specific protein receptors were performed to evaluate binding affinities and ligand–protein interactions, with results highlighting significant interactions within enzyme active sites. These findings emphasize the pivotal role of metal–ligand coordination in enhancing pharmacological properties and contribute valuable insights toward the design of novel therapeutic compounds for use in medicinal chemistry and pharmaceutical research.