A method for controlling alignment of a control loop in an amplifier system includes generating a pilot signal and injecting the pilot signal into the amplifier system. Any uncanceled pilot signal is detected at an output of the control loop. A frequency of the generated pilot signal is detected and is used in adjusting one or more parameters of the control loop. The adjusting is performed at a predetermined direction and with a predetermined step size. A frequency change in the pilot signal in response to the adjusting is detected. The control loop is iteratively aligned by controlling the adjusting based on the detected frequency change, and the step size is determined based on the detected frequency change.