The clear correlation of defect localization by Electroluminescence to nanometer sized defects at Schottky gate contacts of GaN HEMTs are always challenging and limiting the root cause analysis of the stress related electrical degradation of the devices. In this paper a novel approach combining large area planar TEM defect screening followed by cross sectional preparation at identified defect sites is demonstrated to get access to relevant structural damages at the gate. The analysis flow is applied for normally-on GaN HEMT devices with an increased leakage at the Schottky gates observed after electrical stressing. To initiate electrical active degradation these devices were stressed up to significant changes in the electrical performance and then Electroluminescence spots were detected identifying possible defect positions. Metal intrusions into the AlGaN/ GaN stack underneath the Schottky gate contacts of only 20 nm size could be found by the newly combined planar/ cross-sectional analysis flow in good correlation to the EL spot positions. Analytical TEM investigations of the defects reveal Pt and Au inside the semiconductor reaching the 2DEG at a threading dislocation of the HEMT. These intrusions contribute to the gate leakage current and are causing the increased leakage current after electrical testing.