Gold (Au) has been considered catalytically inert for decades, but recent reports have described the ability of Au nanoparticles to catalyze H2O2 decomposition in the Haber-Weiss cycle. Herein, the design and demonstration of a flow-through electro-Fenton system based on an electrochemical carbon nanotube (CNT) filter functionalized with atomically precise Au nanoclusters (AuNCs) is described. The functionality of the device was then tested for its ability to catalyze antibiotic tetracycline degradation. In the functional filters, the Au core of AuNCs served as a high-performance Fenton catalyst; while the AuNCs ligand shells enabled CNT dispersion in aqueous solution for easy processing. The hybrid filter enabled in situ H2O2 production and catalyzed the subsequent H2O2 decomposition to HO·. The catalytic function of AuNCs lies in their ability to undergo redox cycling of Au+/Au0 under an electric field. The atomically precise AuNCs catalysts demonstrated superior catalytic activity to larger nanoparticles; while the flow-through design provided convection-enhanced mass transport, which yielded a superior performance compared to a conventional batch reactor. The adsorption behavior and decomposition pathway of H2O2 on the filter surfaces were simulated by density functional theory calculations. The research outcomes provided atomic-level mechanistic insights into the Au-mediated Fenton reaction.