The copper-catalysed Fenton-like (Cu(II)/H₂O₂) system has garnered attention for its potential in degrading recalcitrant organic contaminants and inactivating microbes in water and wastewater. This study delves into the unique dual-oxidation pathway of the Cu(II)/H₂O₂ system, encompassing the selective oxidation of copper-complexing ligands and the heightened oxidation of non-chelated organic compounds. _L-histidine (His) and benzoic acid (BA) were employed as model compounds for basic biomolecular ligands and recalcitrant organic contaminants, respectively. In the co-presence of His and BA, the Cu(II)/H₂O₂ system rapidly degraded nearly all His complexed with copper ions within 30 seconds, whilst BA degradation exhibited relatively less vigour. Furthermore, BA degradation efficiency was 2.3 times greater than that in the absence of His. The primary oxidant responsible for this distinctive degradation was revealed as cupryl ion (Cu(III)), prevailing over the hydroxyl radical (^•OH). This conclusion was supported by ^•OH scavenging experiments, comparison of hydroxylated BA isomer ratios with a ^•OH generating system (i.e., UV/H₂O₂), electron paramagnetic resonance spectroscopy analysis, and colorimetric Cu(III) detection via the periodate complexation method. Cu(III) species exhibited selective oxidation of His due to its potent chelating properties with copper ions, even in the presence of excess tert-butyl alcohol. This remarkable trait extended to other copper-complexing ligands like _L-asparagine and _L-aspartic acid. Moreover, His presence in the Cu(II)/H₂O₂ system facilitated Cu(II) reduction by H₂O₂, yielding increased Cu(III) production and thus enhancing BA and pharmaceuticals. In essence, this investigation offers profound insights into water treatment strategies, elucidating the intricate oxidation pathways inherent in the Cu(II)/H₂O₂ system.