Three novel copper(II) complexes, [Cu(Gly‐l‐Val)(HPBM)(H2O)]·ClO4·H2O (1), [Cu(Gly‐l‐Val)(TBZ)(H2O)]·ClO4 (2) and [Cu(Gly‐l‐Val)(PBO)(H2O)]·ClO4 (3) (Gly‐l‐Val = glycyl‐l‐valine anion, HPBM = 5‐methyl‐2‐(2′‐pyridyl)benzimidazole, TBZ = 2‐(4′‐thiazolyl)benzimidazole, PBO = 2‐(2′‐pyridyl)benzoxazole), have been prepared and characterized with elemental analyses, conductivity measurements as well as various spectroscopic techniques. The interactions of these copper complexes with calf thymus DNA were explored using UV–visible, fluorescence, circular dichroism, thermal denaturation, viscosity and docking analyses methods. The experimental results showed that all three complexes could bind to DNA via an intercalative mode. Moreover, the cytotoxic effects were evaluated using the MTT method, and the antimicrobial activity of these complexes was tested against Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. The results showed that the activities are consistent with their DNA binding abilities, following the order of 1 > 2 > 3.