We compare the spontaneous emission of C- and M-plane GaN quantum dots embedded in AlN. C-plane dots are characterized by an intense emission with an exceptionally long decay time up to room temperature. In contrast, M-plane dots exhibit a much weaker emission with a very short decay time. In addition, the emission of the C-plane dots temporally evolves on a timescale of seconds, while the emission of the M-plane dots is stable over time. These findings are correlated with the different growth mode and microstructure of C- and M-plane GaN quantum dots.