A system, method, and apparatus for mitigating contamination associated with ion implantation are provided. An ion source, end station, and mass analyzer positioned between the ion source and the end station are provided, wherein an ion beam is formed from the ion source and selectively travels through the mass analyzer to the end station, based on a position of a beam stop assembly. The beam stop assembly selectively prevents the ion beam from entering and/or exiting the mass analyzer, therein minimizing contamination associated with an unstable ion source during transition periods such as a start-up of the ion implantation system.