The pyrimidine based azo-linked Schiff base ligand, 5-benzoyl-1-((E)-(2-hydroxy-3-methoxy-5-((E)phenyldiazenyl)benzylidene)amino)-4-phenylpyrimidin-2(1H)-one (HL), and its transition metal (II) complexes were synthesized and defined by using H-1-NMR, C-13-NMR, Elemental analysis, FT-IR, MS, UV-vis, molar conductance, magnetic susceptibility and thermal analysis techniques. According to the conductance data obtained indicate all of the metal complexes have non-electrolytic nature. Square pyramidal geometry for Pd(II) and octahedral geometry for all the other complexes synthesized was concluded from the electronic absorption spectra and magnetic susceptibility measurements of the complexes. Investigation of the significant infrared bands of the active groups in the ligand and the solid complexes alludes that HL is coordinated to the metal ions ONO tridentate manner. Moreover, the absorption and emission properties of the azo-azomethine based ligand and its complexes were investigated. The results obtained show that fluorescence emissions of the ligand and its metal (II) complexes depend on the type of transition metal ions and the derivatives displayed moderate Stokes' shift values between 44 and 107 nm. All the compounds exhibited superb photostability. Further, antioxidant, antimicrobial and pBR322 plasmid DNA cleavage activities were investigated. All compounds showed good DPPH center dot (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity and complexes of [MnL2]center dot H2O and [NiL2]center dot H2O exhibited excellent metal chelating activity. All the compounds tested demonstrated two strand DNA cleavage activities.