The interaction of Mn with Ge quantum dots (QD), which are bounded by {105} facets, and the strained Ge wetting layer (WL), terminated by a (001) surface, is investigated with scanning tunneling microscopy (STM). These surfaces constitute the growth surfaces in the growth of Mn-doped QDs. Mn is deposited on the Ge QD and WL surface in sub-monolayer concentrations, and subsequently annealed up to a temperature of 400 ° C. The changes in bonding and surface topography are measured with STM during the annealing process. Mn forms flat islands on the Ge{105} facet, whose shape and position are guided by the rebonded step reconstruction of the facet. Voltage-dependent STM images reflect the Mn-island interaction with the empty and filled states of the Ge{105} reconstruction. Scanning tunneling spectra (STS) of the Ge{105} facet and as-deposited Mn-islands show a bandgap of 0.8 eV, and the Mn-island spectra are characterized by an additional empty state at about 1.4 eV. A statistical analysis of Mn-island shape and position on the QD yields a slight preference for edge positions, whereas the QD strain field does not impact Mn-island position. However, the formation of ultra-small Mn-clusters dominates on the Ge(001) WL, which is in contrast to Mn interaction with unstrained Ge(001) surfaces. Annealing to T < 160 °C leaves the Mn-clusters on the WL unchanged, while the Mn-islands on the Ge{105} facet undergo first a ripening process, followed by a volume gain which can be attributed to the onset of intermixing with Ge. This development is supported by the statistical analysis of island volume, size and size distribution. Increasing the annealing temperature to 220° and finally 375 ° C leads to a rapid increase in the Mn-surface diffusion, as evidenced by the formation of larger, nanometer size clusters, which are identified as germanide Mn5Ge3 from a mass balance analysis. This reaction is accompanied by the disappearance of the original Mn-surface structures and de-wetting of Mn is complete. This study unravels the details of Mn–Ge interactions, and demonstrates the role of surface diffusion as a determinant in the growth of Mn-doped Ge materials. Surface doping of Ge-nanostructures at lower temperatures could provide a pathway to control magnetism in the Mn–Ge system.