The ammonia-based molecular beam epitaxy of GaN/(Al, Ga)N quantum dots is investigated using reflection high-energy electron diffraction, atomic force microscopy, transmission electron microscopy and photoluminescence. The main steps of the formation kinetics are identified and the influence of diffusion and evaporation processes on both the quantum dot and the wetting layer morphology is addressed. The correlation between the optical and structural properties of such structures finally allows for the analysis of matter exchanges between the quantum dots and the wetting layer during capping.