A new mononuclear mixed-ligand complex of Ni(II) has been synthesized and structurally characterized by single-crystal X-ray diffraction as compound with the formula of [Ni(4-Cl-pydc)(apym)(H2O)2], where 4-Cl-pydc and apym are 4-chloropyridine-2,6-dicarboxylate and 2-aminopyrimidine, respectively. Also, spectroscopic studies such as FT–IR, UV–Vis, 1H–NMR and thermal analysis (TGA/DTA) were carried out. The fluorescence properties of complex in solvents with different dipole moment were studied. Antimicrobial activities of 4-chloropyridine-2,6-dicarboxylic acid (1), 2-aminopyrimidine (2), complex (3) and nickel (II) nitrate hexahydrate (4) were investigated by disc diffusion and broth microdilution methods against three Gram-positive bacteria namely S. aureus, B. subtilis, S. epidermidis and three Gram-negative bacteria namely E. coli, P. aeruginosa, S. marcescens, as well two fungi strains including Aspergillus niger and Saccharomyces cerevisiae in vitro. The highest antibacterial activity of complex was observed nearly equal to standard drug gentamicin toward S. epidermids. The in vitro anti-proliferative activity of compounds (1)-(4) on H1299 (a human non-small cell lung carcinoma cell line), HepG2 (a human liver hepatocellular carcinoma cell line) and βTC (a mouse beta pancreatic cell line) cell lines was evaluated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) assay and effect of complex on depolarization of mitochondrial membrane (MMP) of all the three cell lines was measured by rhodamine 123. The highest cytotoxic effect of complex was exhibited toward H1299 cell line with IC50 value equal to 10 μM.