This study explores the reactivity of amino acids in the copper-catalysed Fenton-like Cu(II)/H2O2 system, aiming to establish a quantitative correlation between amino acid structure and degradation rates. By experimentally determining degradation rate constants and correlating them with the stability constants of Cu(II)-amino acid complexes, we assess how specific structural features influence oxidative degradation. Density functional theory calculations are employed to evaluate the electron-donating properties of each amino acid, providing molecular-level insights into their interactions with Cu(II) and the resulting reactivity. Our findings offer new perspectives on Cu(III)-mediated disinfection mechanisms, as the study highlights key interactions between Cu(III) and proteins, which may contribute to a better understanding of viral disinfection processes. This research contributes to a broader understanding of how amino acid structure affects reactivity in advanced oxidation processes, with potential applications in the treatment of amino acid-rich wastewater and related environmental challenges.