Magnetic hybrid colloids (MHCs) decorated with different-sized Ag nanoparticles (Ag07@MHC, Ag15@MHC, and Ag30@MHC denote MHCs decorated with ∼7 nm, ∼15 nm, and ∼30 nm AgNPs, respectively) are synthesized and used to investigate their antimicrobial efficacy and mechanism. An MHC (diameter ∼ 0.6 μm) is a cluster of superparamagnetic Fe3O4 nanoparticles (∼10 nm) encapsulated with a silica shell (thickness ∼ 0.1 μm). The Ag30@MHC was prepared using the seed-growth method with Ag seeds self-assembled on the aminopropyl-functionalized MHC, and its surface is covered with AgNPs and Ag+ ions. The Ag07@MHC and Ag15@MHC were prepared using the seeding, coalescing, and growing strategy with Au seeds, and these MHCs released substantially less Ag+ ions than Ag30@MHC due to the contribution of the Au core. The Ag30@MHC exhibited the greatest antimicrobial efficacy towards E. coli CN13 (6-log reduction) and the bacteriophage MS2 (2-3 log reduction) due to the synergistic effect of the 3D architecture decorated with AgNPs and Ag+ ions as well as the already-known effects of free AgNPs. On the 3D architecture, the AgNPs abstract Mg2+ or Ca2+ ions from the bacterial membrane and the Ag+ ions grab the microorganisms by forming a complex with the thiol groups imbedded in the membrane, which bites away bacteria and completely ruptures the cell structure. The Ag30@MHC is easily collectible from the reaction mixture using an external magnet without detachment of AgNPs, and it is re-dispersible. Overall, Ag30@MHC is believed to be a promising antimicrobial material for practical applications.