An improved system for tuning a motor controller is disclosed. The controller gains are initially set based on the measured frequency response for the controlled system. A desired level of performance is defined by setting a desired phase margin and a desired gain margin to be observed in the frequency response. An improved method of determining the frequency response provides for a reduced computational intensity. The initial tuning routine uses the frequency response to set not only controller gains, but also settings for filters in the control module. Having obtained the desired level of performance from the initial tuning, the motor drive executes an adaptive tuning routine while controlling the motor. The adaptive tuning routine tracks changes in the operating performance and adjusts the filter settings or the controller gains to return operation to within the desired level of performance while the motor continues to operate.