Examples described herein provide a rotary system that includes a rotor having an axis of rotation, a position sensor to measure an angular position of the rotor with respect to the axis of rotation, and a processing system to perform operations. The operations include receiving an output from the position sensor, the output being a measure of an angular position of the rotor with respect to the axis of rotation. The operations further include generating, based on the output from the position sensor, an error signal, an estimated angular velocity, and an estimated position. The operations further include performing a position sensor harmonic adaptation based at least in part on the error signal, the estimated angular velocity, and the estimated position to generate adaptation coefficients. The operations further include performing a position sensor harmonic compensation based on the adaptation coefficients and the estimated position to generate a difference in position.