Embodiments relate to a grid short clearing system is provided for gridded ion beam sources used in industrial applications for materials processing systems that reduces grid damage during operation. In various embodiments, the ion source is coupled to a process chamber and a grid short clearing system includes methods for supplying a gas to the process chamber and setting the gas pressure to a predetermined gas pressure in the range between 50 to 750 Torr, applying an electrical potential difference between each adjacent pair of grids using a current-limited power supply, and detecting whether or not the grid shorts are cleared. The electrical potential difference between the grids is at least 10% lower than the DC electrical breakdown voltage between the grids with no contaminants.