Nanofiltration (NF) membranes have been widely applied in wastewater treatment. However, their wider applications and further popularization are still hindered owing to severe membrane fouling and decreasing cleaning efficiency. In this study, Fenton/Fenton-like agents with a strong foulant degradation ability are prepared and selected, and their influence on the physicochemical properties of polyamide (PA) NF membranes and cleaning efficiency are systematically investigated. It is found that the secondary fouling caused by ferric hydroxide precipitates makes the conventional Fenton agent unsuitable for membrane cleaning. Then, a Fenton-like agent with magnetic Fe₃O₄ nanoparticles modified by γ-poly-glutamic acid (γ-PGA) and L-histidine (L-His) is prepared for membrane cleaning with a low concentration of hydrogen peroxide (<1 mM). Therein, the γ-PGA coating significantly inhibits the agglomeration of nanoparticles by improving their hydrophilicity/dispersibility and reduces their adsorption on the membrane as well as metal ion leaching. More importantly, the imidazole functional groups of L-histidine endow Fe₃O₄ nanoparticles with a higher affinity for hydrogen peroxide, thus ameliorating their catalytic activity for foulant degradation. Combining alkaline cleaning and Fenton-like catalysis cleaning, the stubborn pore fouling can be almost fully removed (100% and 95% for dead-end and cross-flow filtrations, respectively) because the alkali-induced pore swelling effect would enlarge the membrane pores and enhance the mass transfer of free radicals (˙O₂⁻ and ˙OH) into the pores and the release of oxidated foulants. Such a magnetic cleaning agent can be easily recovered and reused for green and sustainable membrane cleaning.