One or more embodiments are described for preventing controller windup in a motion control system. An example system includes a regulator that receives an input command to adjust a motion control variable of a mechanical system that includes a motor, the regulator configured to generate a first torque command based on the input command and an output torque from the motor. The system further includes a motor control module that receives the first torque command to generate an input torque command that is sent to the motor. The system further includes an anti-windup module that is configured to generate an anti-windup command based on the first torque command and the output torque, the anti-windup command being added to the input command that is sent to the regulator.