Abstract We studied the disinfection efficacy of boron-doped electrodes on Escherichia coli-contaminated water-based solutions in three different electrolytes, physiological solution (NaCl), phosphate buffer (PB), and phosphate buffer saline (PBS). The effect of the electrochemical oxidation treatment on the bacteria viability was studied by drop and spread plate cultivation methods, and supported by optical density measurements. We have found that bacterial suspensions in NaCl and PBS underwent a total inactivation of all viable bacteria within 10 min of the electrochemical treatment. By contrast, experiments performed in the PB showed a relatively minor decrease of viability by two orders of magnitude after 2 h of the treatment, which is almost comparable with the untreated control. The enhanced bacterial inactivation was assigned to reactive chlorine species, capable of penetrating the bacterial cytoplasmic membrane and killing bacteria from within.