A disk drive is disclosed comprising a disk and a head actuated over the disk by a voice coil motor (VCM) comprising a voice coil, wherein the VCM is controlled by a VCM control loop comprising an IR voltage detector. The IR voltage detector is updated by measuring a first back EMF voltage of the voice coil, and after measuring the first back EMF voltage, applying a first control current to the voice coil for a first interval and applying a second control current to the voice coil for a second interval. After the second interval, a second back EMF voltage is measured, and a delta voltage is computed relative to a difference between the first back EMF voltage and the second back EMF voltage. The IR voltage detector is adjusted in response to the delta voltage and at least one of the first and second control currents.