The structural analysis of GaN and Al x Ga1-x N/GaN heterostructures grown by metalorganic vapor phase epitaxy in the presence of Mn reveals how Mn affects the growth process and in particular, the incorporation of Al, the morphology of the surface, and the plastic relaxation of Al x Ga1-x N on GaN. Moreover, the doping with Mn promotes the formation of layered Al x Ga1-x N/GaN superlattice-like heterostructures, which opens wide perspectives for controlling the segregation of ternary alloys during the crystal growth and for fostering the self-assembling of functional layered structures.