A combine side-shaking control system and a method for controlling operation of a side-shaking mechanism in a combine. The control system includes at least one sieve for separating crop material from other materials and a movable side-shaking mechanism coupled to the at least one sieve and configured to move the at least one sieve in a side-to-side motion. The control system also includes at least one sensor for sensing at least one operating condition of a combine system. The control system further includes a controller for receiving the at least one operating condition and causing the side-shaking mechanism to stop moving the at least one sieve in the side-to-side motion or start moving the at least one sieve in the side-to-side motion based on the at least one operating condition.