A control system for a harvester having a primary crop cleaner for cleaning a cut crop, and a secondary cleaner for cleaning the cut crop downstream of the primary crop cleaner. The control system includes a processor, a memory, and a human-machine interface. The processor is configured to receive an input corresponding to a desired cleaning level of the crop, monitor an actual cleaning level, control the primary crop cleaner based at least in part on feedback from monitoring the actual cleaning level and including adjusting a speed of the primary crop cleaner to move the actual cleaning level of the crop during harvester operation towards the desired cleaning level of the crop, monitor an error between the desired cleaning level and the actual cleaning level during control of the primary crop cleaner, and control the secondary crop cleaner based at least in part on the error.