A system and method of improving the performance and extending the lifetime of an ion source is disclosed. The ion source includes an ion source chamber, a suppression electrode and a ground electrode. In the processing mode, the ion source chamber may be biased to a first positive voltage, while the suppression electrode is biased to a negative voltage to attract positive ions from within the chamber through an aperture and toward the workpiece. In the cleaning mode, the ion beam is defocused so that it strikes the suppression electrode and the ground electrode. The voltages applied to the ion source chamber and the electrodes are pulsed to minimize the possibility of glitches during this cleaning mode.