We compare the quality factor values of the whispering gallery modes of microdisks (μ-disks) incorporating GaN quantum dots (QDs) grown on AlN and AlGaN barriers by performing room temperature photoluminescence (PL) spectroscopy. The PL measurements show a large number of high Q factor resonant modes on the whole spectrum, which allows us to identify the different radial mode families and to compare them with simulations. We report a considerable improvement of the Q factor, which reflects the etching quality and the relatively low cavity loss by inserting QDs into the cavity. GaN/AlN QDs-based μ-disks show very high Q values (Q>7000) whereas the Q factor is only up to 2000 in μ-disks embedding QDs grown on the AlGaN barrier layer. We attribute this difference to the lower absorption below bandgap for AlN barrier layers at the energies of our experimental investigation.