In this work, we have synthesized pyrimidine derivatives of Schiff base ligand 2-(4,6-dimethoxypyrimidin-2-ylimino)methyl)-6-methoxyphenol (DPMM) stabilized copper nanoparticles (DPMM-CuNPs) and nickel nanoparticles (DPMM-NiNPs) by modified Brust-Schiffrin technique as two step phase transfer assisted method and confirmed by UV–Visible, SEM and TEM analysis. The free radical scavenging activity of DPMM, DPMM-CuNPs &DPMM-NiNPs with 2, 2′-diphenylpicryl hydrazyl (DPPH), hydrogen peroxide (H2O2) super oxide dismutase (SOD) and nitric oxide (NO) shows that the antioxidant activity of DPMM-CuNPs is higher than DPMM &DPMM-NiNPs. Interaction study of DPMM-CuNPs &DPMM-NiNPs with CT-DNA has been investigated by absorption spectral titration, fluorescence studies, cyclic voltammetry and viscometric measurements. Dose dependent antibacterial and antifungal studies of DPMM-CuNPs & DPMM-NiNPs against five different bacteria Shigella sonnei, Staphylococcus aureus, Escherichia coli, Klepsiella pneumoniae, Pseudomonas fluoroscens and five different fungi Aspergillus niger, Candida albicans, Candida tropicalis, Mucor indicus and Rhizopus show that the compounds have significant antibacterial and antifungal activity. Cytotoxicity studies of DPMM-CuNPs &DPMM-NiNPs on human breast cancer cell line (MCF-7) were studied by 3-(4, 5-dimethylthiazol-2-yl-)-2, 5-diphenyltetrazolium bromide (MTT) assay. 50% cell viability was found at 25μg/mL for DPMM-CuNPs and 300μg/mL for DPMM-NiNPs. Collective biological results reveal that the synthesized DPMM-CuNPs is more biologically active than DPMM-NiNPs.