This manuscript describes the synthesis (based on the intermatrix synthesis (IMS) method), optimization, and application to bacterial disinfection of Ag@Co polymer metal nanocomposite materials with magnetic and bactericidal properties. This material showed ideal bactericide features for being applied to bacterial disinfection of water, particularly (1) an enhanced bactericidal activity (when compared with other nanocomposites only containing Ag or Co nanoparticles), with a cell viability close to 0% for bacterial suspensions with an initial concentration below 105 colony forming units per milliliter (CFU/mL) after a single pass through the material, (2) capacity of killing a wide range of bacterial types (from coliforms to Grampositive bacteria), and (3) a long performance-time, with an efficiency of 100% (0% viability) up to 1 h of operation and higher than 90% during the first 24 h of continuous operation. The nanocomposite also showed a good performance when applied to water samples from natural sources with more complex matrices with efficiencies always higher than 80%.