The synthesis of germanene on semiconducting substrates such as MoS 2 has revealed that it exhibits a Vshaped density of states around the Fermi level, indicating the presence of Dirac electrons. Further experiments demonstrated that charge inhomogeneities of germanene on MoS 2 appear as n-and p-type doped regions, the origin of which is not well understood. In this paper, by means of density functional theory calculations, we study germanene deposited on MoS 2 considering various defect types and a variety of stacking configurations. We find that some native defects typical to MoS 2 samples lead to the charge transfer between germanene and MoS 2 . Unlike vacancies and antisite defects, substitution of molybdenum by group IV-V and VII transition metal atoms does not lead to any midgap states, and appears as a plausible explanation for the experimentally observed charge puddles. Our results shed light on the mechanism of breaking the charge neutrality in Dirac materials without altering their electronic properties, which could be important for the realization of lateral p-n junctions based on two-dimensional materials.