We compare the effectiveness of in situ thermal cleaning with that of Al-assisted cleaning of native surface oxides of bulk AlN for homoepitaxial growth by molecular beam epitaxy. Thermal deoxidation performed at 1450 °C in vacuum results in voids in the AlN substrate. On the other hand, Al-assisted deoxidation at ≈900°C results in high-quality AlN homoepitaxy, evidenced by clean and wide atomic terraces on the surface and no extended defects at the growth interface. This study shows that Al-assisted in situ deoxidation is effective in removing native oxides on AlN, providing a clean surface to enable homoepitaxial growth of AlN and its heterostructures; furthermore, it is more attractive over thermal deoxidation, which needs to be conducted at much higher temperatures due to the strong bonding strength of native oxides on AlN.