A system to control an ion beam in an ion implanter includes a detector system to detect a plurality of beam current measurements of the ion beam at a first frequency and an analysis component to determine a variation of the ion beam based upon the plurality of beam current measurements, the variation corresponding to a beam current variation of the ion beam at a second frequency different from the first frequency. The system also includes an adjustment component to adjust the ion beam in response to an output of the analysis component to reduce the variation, wherein the analysis component and the adjustment component are configured to dynamically reduce the variation of the ion beam below a threshold value while the ion beam is generated in the ion implanter.