A control system using flux feedback is disclosed. The control system may be for an electric motor of a machine. The control system may have a control mechanism configured to selectively provide electricity from a generator to the electric motor. The control system may also have at least one first sensor configured to generate a signal indicative of a state of a magnetic flux produced by the electric motor. The control system may further have a controller in communication with the control mechanism and the first sensor, the controller configured to adjust operation of the control mechanism based on the signal.