Phase-separated semiconductor systems hosting magnetic nanocrystal (NCs) are attracting increasing attention, due to their potential as spintronic elements for the next generation of devices. Owing to their morphology- and stoichiometry-dependent magnetic response, self-assembled -GayFe4yN NCs embedded in a Fe -doped GaN matrix, are particularly versatile. It is studied and reported here, how the tuning of relevant growth parameters during the metalorganic vapour phase epitaxy process affects the crystalline arrangement, size, and shape of these self-assembled nanostructures. In particular, it is found that the Ga-flow provided during the -doping, determines the amount of Fe incorporated into the layers and the spatial density of the NCs. Moreover, the in-plane dimensions of the NCs can also be controlled via the Ga-flow, conditioning the aspect-ratio of the embedded nanostructures. These findings are pivotal for the design of nanocrystal arrays with on-demand size and shape, essential requirements for the implementation into functional devices.