In the Fe-doped GaN phase-separated magnetic semiconductor Ga[Formula: see text]FeN, the presence of embedded [Formula: see text]-[Formula: see text]N nanocrystals determines the magnetic properties of the system. Here, through a combination of anomalous X-ray diffraction and diffraction anomalous fine structure, the local structure of Ga in self-assembled face-centered cubic (fcc) [Formula: see text]-[Formula: see text]N nanocrystals embedded in wurtzite GaN thin layers is investigated in order to shed light onto the correlation between fabrication parameters, local structural arrangement and overall magnetic properties of the material system. It is found, that by adjusting the growth parameters and thus, the crystallographic surroundings, the Ga atoms can be induced to incorporate into 3c positions at the faces of the fcc crystal lattice, reaching a maximum occupancy of 30%. The magnetic response of the embedded nanocrystals is ferromagnetic with Curie temperature increasing from 450 to 500 K with the Ga occupation. These results demonstrate the outstanding potential of the employed experimental protocol for unravelling the local structure of magnetic multi-phase systems, even when embedded in a matrix containing the same element under investigation.