A novel disinfection method with recyclable magnetic nanoparticles is presented to optimize the traditional method with metal ions upon virus contamination. In this study, magnetic nanoparticles with permanently confined micelle arrays (Mag-PCMA) were coated with Ag + , Cu 2+ , and Fe 3+ via sorption to increase the ζ potential from negative to positive. Three types of Mag-PCMA coated with different metal ions (Mag-PCMA-MI) were mixed with a model virus, MS-2, to evaluate their disinfection ability. MS-2 removal by Mag-PCMA-MI was influenced by the concentration of Mag-PCMA-MI and contact time. The MS-2 removal efficiency reached 99% with 0.5 g/L Mag-PCMA-Ag after 30 min. Removal with Mag-PCMA-MI remains stable under most environmental conditions (e.g., water hardness and the presence of natural organic matter), except for a change in pH, which decreases removal efficiency (0.43% for Mag-PCMA-Ag, 0.35% for Mag-PCMA-Cu, and 0.28% for Mag-PCMA-Fe) for an increase in pH from 6 to 8. The reuse of Mag-PCMA-MI can be achieved by simply rinsing the nanoparticles with deionized water to remove the inactivated virus after disinfection, and the removal efficiency remains >99.8% for all three Mag-PCMA-MI after five continuous cycles, highlighting the recyclability of the process.