Nickel germanide is deemed an excellent material system for low resistance contact formation for future Ge device modules integrated into mainstream, Si-based integrated circuit technologies. In this study, we present a multi-technique experimental study on the formation processes of nickel germanides on Ge(001). We demonstrate that room temperature deposition of ∼1 nm of Ni on Ge(001) is realized in the Volmer-Weber growth mode. Subsequent thermal annealing results first in the formation of a continuous NixGey wetting layer featuring well-defined terrace morphology. Upon increasing the annealing temperature to 300 °C, we observed the onset of a de-wetting process, characterized by the appearance of voids on the NixGey terraces. Annealing above 300 °C enhances this de-wetting process and the surface evolves gradually towards the formation of well-ordered, rectangular NixGey 3D nanostructures. Annealing up to 500 °C induces an Ostwald ripening phenomenon, with smaller nanoislands disappearing and larger ones increasing their size. Subsequent annealing to higher temperatures drives the Ni-germanide diffusion into the bulk and the consequent formation of highly ordered, {111} faceted Ni-Ge nanocrystals featuring an epitaxial relationship with the substrate Ni-Ge (101); (010) || Ge(001); (110).