© 2022 Elsevier LtdMn, Fe, and Cu ions, when doped into ZnO nanocrystals, impart magnetic phenomena to their semiconducting property. Although notable in the dilute magnetic semiconductor community, transition metal (TM) ion-doped ZnO lacks investigations that inform researchers on the local lattice structure around the dopant ion, its spin-exchange phenomena, and the interaction between its intrinsic defects and the doped metal ion. The current study presents a detailed multi-frequency (X- and Q-band) EPR investigation that clarifies the localization of the dopant ion, its site symmetry, and the formation of intrinsic-extrinsic defect complexes in ZnO:TM. The incorporation of TM ion is observed to modify the intrinsic defect structure of ZnO nanocrystals. Particularly, a deviation from the core-shell model is observed for ZnO:TM, and the appearance of intrinsic-extrinsic defect complexes that may contribute to a peculiar spin-exchange phenomenon are noticed. Additionally, the localization as observed from the resonance lines of defect complexes comprising Cu2+ is different from those of Mn2+ and Fe3+, showing charge selective substitutions in the matrix.