We report a correlative microscopy study of a sample containing three stacks of InGaN/GaN quantum dots (QDs) grown at different substrate temperature, each stack consisting of 3 layers of QDs. Decreasing the substrate temperature along the growth axis leads to the proliferation of structural defects. However, the luminescence intensity increases towards the surface, in spite of the higher density of threading dislocations, revealing that the QD layers closer to the substrate behave as traps for non-radiative point defects. During atom probe tomography experiments combined with in-situ micro-photoluminescence, it was possible to isolate the optical emission of a single QD located in the topmost QD stack, closer to the sample surface. The single QD emission line displayed a spectral shift during the experiment confirming the relaxation of elastic strain due to material evaporation during atom probe tomography.