A control circuit optimizes the track seeking operation of a disk drive by automatically adjusting the phase margin of a compensator circuit that generates a control signal used to drive the actuator of the disk drive to optimize the actual performance of the drive during track seeking operations. Parametric values of coefficients associated with the compensation circuit used for driving the head of the disk drive are adjusted responsive to the determination of the system phase margin to change the phase margin and bring it within a desired range. More specifically, the present invention provides a method and apparatus for automatically controlling the phase margin in a compensation control circuit for a disk drive having a head driven by an actuator. The head is driven with a control signal that is generated by a compensator circuit. Feedback from the head is employed to create a position signal, which is used to generate a position error signal. The position error signal is combined with a disturbance signal of predetermined frequency. The resulting signal is fed into the compensator circuit, which has a transfer function that can be expressed mathematically in terms of one or more coefficients. The phase margin of the system is computed by taking the phase difference between the disturbance signal and the component of the position error signal that has the same frequency as the disturbance signal. The values of the compensator circuit coefficient are adjusted to bring the phase margin within an acceptable range.