A deposit cleaning system for removing deposits from interior surfaces of ion sources and/or electrodes includes a fluorine source, a throttle mechanism, and a controller. The fluorine source supplies fluorine to the ion source as a cleaning material. The throttle mechanism mitigates loss of fluorine through a source aperture of the ion source by at least partially covering the source aperture. The controller controls the supply and flow rate from the fluorine source to the ion source and also controls the positioning of the throttle mechanism.