He implantation was performed at RT and 550 °C into AlN epitaxial films. The resulting microstructural damage and elastic strain were investigated using TEM and XRD. Basal stacking faults, clusters of point defects and bubbles aligned along (0001) planes are observed at both temperatures. Apart from slight variations of size and densities of defects, no significant difference is observed on the microstructure after implantation at RT and 550 °C. In particular, He bubbles are observed with similar size, showing that the long-range migration of vacancies is not triggered at 550 °C. An important effect of He on the enhancement of damage and strain build-up during implantation is evidenced. He bubbles are observed to strongly favor the nucleation of extended defects, both basal stacking faults and point defect clusters, which results from the increase of free interstitial concentration due to stabilization of vacancies by He that could be enhanced by the bubble growth by loop punching or trap mutation to relieve the gas pressure. At an earlier stage of implantation-induced damage, the presence of He is also seen to induce a strong increase of strain with increasing implantation temperature, whilst efficient point defect recombination takes place in the regions free of He, or with low concentration of He, resulting in a decrease of strain. The strong increase of strain with increasing temperature in the deep implanted region, concomitant with a strong reduction of scattered intensity, is ascribed to the growth of He–V complexes, probably induced by a thermally enhanced mobility of He, and only occurs for sufficient He concentration.