Changing the morphology of the growing surface and the nature of residual impurities in (Ge,Mn) layers dramatically changes nanospinodal decomposition, i.e., the morphology of ferromagnetic Mn-rich inclusions. By this way, we are able to control the magnetotransport properties of (Ge,Mn) films. By using different substrates and substrate preparation, we have indeed obtained p -type layers with nanocolumns, either parallel or entangled, and n -type layers with spherical clusters. Holes exhibit an anomalous Hall effect and electrons exhibit a tunneling magnetoresistance, both with a clear dependence on the magnetization of the Mn-rich inclusions; holes exhibit orbital MR and electrons show only the normal Hall effect, and an additional component of magnetoresistance due to weak localization, all three being independent of the magnetic state of the Mn-rich inclusions. Identified mechanisms point to the position of the Fermi level of the Mn-rich material with respect to the valence band of germanium as a crucial parameter for the control and the optimization of magnetotransport in such hybrid layers.