Thermal healing of focused ion beam-implanted defects in GaN is investigated by off-axis electron holography in TEM. The data reveal that healing starts at temperatures as low as about 250 degrees C. The healing processes result in an irreversible transition from defect-induced Fermi level pinning near the VB toward a midgap pinning induced by the crystalline-amorphous transition interface. Based on the measured pinning levels and the defect charge states, we identify the dominant defect type to be substitutional carbon on nitrogen sites.