Growing InGaN quantum dots (QDs) at the apex of hexagonal GaN pyramids is an elegant approach to achieve a deterministic positioning of QDs. Despite similar synthesis procedures by metal organic chemical vapor deposition, the optical properties of the QDs reported in the literature vary drastically. The QDs tend to exhibit either narrow or broad emission lines in the micro-photoluminescence spectra. By coupled microstructural and optical investigations, the QDs giving rise to narrow emission lines were concluded to nucleate in association with a (0001) facet at the apex of the GaN pyramid.