A data storage device is disclosed comprising a first plurality of heads actuated over a first subset of disk surfaces by a first servo control loop comprising a first coarse actuator and a first fine actuator, and a second plurality of heads actuated over a second subset of the disk surfaces by a second servo control loop comprising a second coarse actuator and a second fine actuator. A plurality of access commands are received, wherein each access command is associated with one of the heads. While executing a first access command using the first servo control loop, a disturbance is ramped while injecting the disturbance into the second servo control loop, and the second fine actuator is calibrated based on the disturbance.