Effective removal of toxic metal–organic ligand complexes from contaminated water is still a challenging task. Here, we found that ozonation could achieve efficient degradation of Cu(II)-EDTA and simultaneous removal of Cu(II) from acidic solution (pH 3.1–6.3) as well as from an electroplating effluent (pH 3.6). A complete Cu-EDTA and 75–80% of TOC removal could be achieved from a synthetic solution at the initial Cu(II) of 64 mg L−1 and ozone dosage of 30 mg min−1 L−1. The acidic pH changed to circumneutral during ozonation, resulting in 90–97% of Cu(II) removal through precipitation finally. HO-mediated oxidation was predominantly responsible for the degradation of Cu-EDTA, as proved by the radical scavenging experiments and electron paramagnetic resonance. Based on the evolution of HPLC spectra and HPLC–MS analysis, a stepwise decarboxylation (i.e., cleavage of N–C bond) was found to responsible for the ozonation of Cu-EDTA, where six intermediates/products were identified. Thus, a plausible mechanism involving decarboxylation followed by Cu(II) precipitation was proposed. Ozonation could also realize efficient removal of Cu(II)-EDTA, Cu(II) and TOC from a realistic electroplating effluent. We believe this study would provide a simple and promising option for water decontamination from toxic metal–organic ligand complexes.