The current study evaluated the disinfection efficiency of free chlorine and chloramine for microorganisms on various pipe materials, such as copper, galvanized steel, carbon steel, and stainless steel. In addition, the effect of internal pipe corrosion and corrosion inhibitors on the bactericidal efficiency was evaluated using a simulated loop. For disinfection with a phosphate corrosion inhibitor, chloramination was found to be more effective than chlorination due to its persistence. Free chlorine disinfection was optimized with a high phosphoric acid concentration, while chloramine disinfection was optimized with a high phosphoric acid or low polyphosphate concentration. In simulated copper and galvanized steel loop tests, chloramination with phosphoric acid was demonstrated to be more effective.