The frequency-dependent properties of Mn-doped (3–5 at.%) aligned zinc oxide (Mn–ZnO) nanorods, synthesized by hybrid wet chemical route onto glass substrates, were investigated by bias-dependent impedance spectroscopy. No peak of Mn cluster/secondary phases was detected in the X-ray diffraction traces of the samples. XPS studies show the presence of oxygen vacancies in Mn–ZnO nanorods and Mn in Mn 2+ and Mn 4+ charge states. Although X-ray diffraction/X-ray photoelectron spectroscopy does not give any indication of the presence of metal clusters in the samples, bias-dependent impedance spectroscopy demonstrates significant sensitivity to the formation of Mn clusters in Mn–ZnO nanorods.