The morphological stability during activation annealing of Mg-implanted GaN layers (2 ?m thick) grown on Si (111) is studied for several protective layers and fluencies in the 1013–1015 at. cm?2 range. We show that a thin capping, composed of a few nanometer thick AlN and SiNx stacks grown in situ just after GaN deposition, provides a good solution to retain flat morphology and no strain cracking up to 1 h annealing at 1100 °C in N2. These results are compared to thicker protective stackings with AlN layers of Si3N4 or SiO2 deposited after the implantation that withstand a thermal budget of up to 1 h at 1200 °C in N2. The efficiency of these different cap layers to limit GaN damage during high-temperature annealing is studied as well as the impact of Mg implantation process on the cap resilience. The quality of the GaN sublayer is studied by low-temperature photoluminescence to analyze structural/optical defects and Mg related complexes. X-ray diffraction is performed to evaluate residual strains at the different process stages. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim