A new series of bio active Cu(II) and Zn(II) complexes [CuL(phen)](OOCCH3) (1), [ZnL(phen)](OOCCH3) (2), [CuL(bpy)](OOCCH3) (3), [ZnL(bpy)](OOCCH3) (4) have been synthesized using the pyrimidine derivative Schiff base (HL) [HL = 2-(4,6-dimethylpyrimidin-2-ylimino)methyl)-4-nitrophenol], 1,10-phenanthroline (phen), 2,2’-bipyridine (bpy) and acetate salts of Cu(II) and Zn(II). UV-Visible, FT-IR, 1H-NMR, ESR, elemental analysis, molar conductance and EI-MS spectral techniques have been used to endorse the square planar geometry for the complexes 1–4. The optimized molecular structure and the harmonic vibrational frequencies have been scrutinized by DFT methods. The antibacterial and antifungal activity of Schiff base (HL) and complexes 1–4 indicates that complex 1 acts as good antimicrobial agent against microbial strains than HL, complexes 2–4 and standard drugs streptomycin and nystatin. DNA cleavage study of the complexes 1–4 exposes that complexes 1 and 3 spectacle good cleaving agent than complexes 2 and 4. The interaction of complexes 1–4 with CT DNA using absorption, emission and viscometric measurements signifies that complexes 1–4 bind via an intercalation mode. The highest binding constants (K b) for the complex 1 is confirmed as 7.83 × 103 M−1 and 2.98 × 104 M−1 by absorption and emission spectrum respectively. These experimental observations were found to be close to the theoretical observations investigated by the molecular docking technique. Antioxidant property of the complexes 1–4 using DPPH assay clinches that complex 1 produces significant scavenging effect than other compounds. The result of in vitro cytotoxicity of the Schiff base (HL) and complexes 1–4 shows that complex 1 shows better ability to inhibit the growth of cancer cells. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.