Clean water free of bacteria is a precious resource in areas where no centralized water facilities are available. Conventional chlorine disinfection is limited by chemical transportation, storage, and the production of carcinogenic by-products. Here, a smartphone-powered disinfection system is developed for point-of-use (POU) bacterial inactivation. The integrated system uses the smartphone battery as a power source, and a customized on-the-go (OTG) hardware connected to the phone to realize the desired electrical output. Through a downloadable mobile application, the electrical output, either constant current (20–1000 µA) or voltage (0.7–2.1 V), can be configured easily through a user-friendly graphical interface on the screen. The disinfection device, a coaxial-electrode copper ionization cell (CECIC), inactivates bacteria by low levels of electrochemically generated copper with low energy consumption. The strategy of constant current control is applied in this study to solve the problem of uncontrollable copper release by previous constant voltage control. With the current control, a high inactivation efficiency of E. coli (~6 logs) is achieved with a low level of effluent Cu (~200 µg L−1) in the water samples within a range of salt concentration (0.2–1 mmol L−1). The smartphone-based power workstation provides a versatile and accurate electrical output with a simple graphical user interface. The disinfection device is robust, highly efficient, and does not require complex equipment. As smartphones are pervasive in modern life, the smartphone-powered CECIC system could provide an alternative decentralized water disinfection approach like rural areas and outdoor activities.