Polyphenolic compounds such as flavonoids are closely linked with therapeutical approaches in oxidative stress related diseases mainly because of their antioxidant and metal binding properties. The formation of metal ion complexes can significantly improve the biological activity of the parent flavonoid e.g. during DNA-intercalation process with consequences on its therapeutical functions. The aim of this work is to describe the interaction between the studied set of structurally different flavonoids (kaempferol, luteolin, fisetin and apigenin) and Cu(II) ions. Formation of stable Cu(II) complexes of kaempferol, luteolin, fisetin and apigenin is confirmed by UV-Vis spectroscopy in methanolic solution. Changes in the Vis-region clearly document the complexation of Cu(II) ions, what is further confirmed by the calculated TD-DFT electronic transitions. According to the calculated DFT energies the Cu acceptor site preference decreases in the order Cu1 > Cu2 > Cu3. The molecular docking studies demonstrate a better intercalating ability towards the DNA of Cu(II)–flavonoid complexes when compared to free flavonoids. In particular, Cu1–apigenin and Cu1–kaempferol are identified as the most promising intercalating agents. The obtained results indicate the mechanism by which studied Cu(II)–flavonoid complexes are formed and may interact with DNA, what predispose such substances to act as potential therapeutics with DNA as a target molecule.