A first adaptive fly height measurement is performed between a read/write head and a recording medium during a stage of qualification testing of a magnetic disk drive. A second adaptive fly height measurement of the read/write head is performed during a subsequent stage of the qualification testing. In response to determining that a fly height decrease between the first and second adaptive fly height measurements is above a threshold value, a mitigation operation is performed to remove a contaminant from a media-facing surface of the read/write head.