A hard disk drive or other disk-based storage device comprises a storage disk, a read/write head configured to read data from and write data to the disk, and control circuitry coupled to the read/write head and configured to process data received from and supplied to the read/write head. The control circuitry comprises calibration circuitry configured to vary a phase of a clock signal as a test pattern is written to the storage disk as part of a calibration procedure, and disk locked clock circuitry coupled to the calibration circuitry and configured to obtain phase lock between the clock signal and a timing pattern on a surface of the storage disk. The calibration circuitry is further configured to determine an initial phase update value to be applied by the disk locked clock circuitry in a control loop as the phase of the clock signal is varied as part of the calibration procedure.