Electrochemical disinfection has emerged as one of the most promising alternatives to the conventional disinfection of water in many applications. Although the mechanism of electrochemical disinfection has been largely attributed to the action of electro-generated active chlorine, the role of other oxidants, such as the reactive oxygen species (ROS) *OH, O3, H2O2, and *O2- remains unclear. In this study, we examined the role of ROS in the electrochemical disinfection using a boron-doped diamond (BDD) electrode in a chloride-free phosphate buffer medium, in order to avoid any confusion caused by the generation of chlorine. To determine which species of ROS plays the major role in the inactivation, the effects of several operating factors, such as the presence of *OH scavenger, pH, temperature, and the initial population of microorganisms, were systematically investigated. This study clearly showed that the *OH is the major lethal species responsible for the E. coli inactivation in the chloride-free electrochemical disinfection process, and that the E. coli inactivation was highly promoted at a lower temperature, which was ascribed to the enhanced generation of O3.