Clustered nanoassemblies of Mn doped ZnO and co-doped ZnO (Mn, Sn co-doped ZnO; Mn, Sb co-doped ZnO; and Mn, Bi co-doped ZnO) were prepared by refluxing their respective precursors in diethylene glycol medium. The co-doping elements, Sn, Sb and Bi exist in multi oxidation states by forming Zn–O–M (M = Sb, Bi and Sn) bonds in hexagonal wurtzite nanostructure. The analyses of detailed structural characterization performed by XRD, X-ray photoelectron spectroscopy (XPS) and high resolution transmission electron microscopy (HRTEM), show that co-doping ions are successfully incorporated into the ZnO nanostructure and do not appear as precipitates or secondary phases. HRTEM analysis also confirmed the oriented attachment of nanocrystals as well as their defect structures. The formation/activation of higher amount of intrinsic host defects, for instance, oxygen vacancies in co-doped ZnO as compared to Mn doped ZnO sample is evident from Raman spectra. The doped and co-doped samples exhibit ferromagnetic like behavior at room temperature presumably due to the presence of defects. Specifically, it has been observed that the incorporation of dopant and co-dopants into ZnO structure can modulate the local electronic structure due to the formation/activation of defects and hence, cause significant changes in their structural, vibrational, optical and magnetic properties.