Thanks to its low resistivity (22 µΩ cm), low formation temperature (300-500 °C) and low Ge consumption, NiGe is deemed as a promising candidate as source/drain contact material. However, the agglomeration of NiGe films at high temperature hinders their extensive applications in Ge-based devices. In this work, prior-germanidation fluorine implantation is employed to improve the thermal stability of NiGe films, as well as to form a shallow n-Ge junction simultaneously. As-formed NiGe films with and without fluorine were characterized by means of sheet resistance measurement, X-ray diffraction (XRD), scanning electron microscopy (SEM), and secondary ion mass spectrometry (SIMS). It is found that compared to NiGe films without fluorine, the thermal stability of NiGe films with fluorine can be improved by approximately 50 °C. Moreover, the junction depth of n-Ge with fluorine is approximately 8 nm shallower than that without fluorine. The aggregation of fluorine atoms at NiGe grain boundaries and at the NiGe/Ge interface is thought to be responsible for enhanced thermal stability, as well as the increase in sheet resistance of as-formed NiGe films.