Germanium has recently gained attention as an alternative to silicon in electronics, with particular interest in dewetting processes for photonics. Dewetted surfaces, where germanium is present at 20-30%, are crucial as they enable the development of nanostructures for various applications. In this context, stable and high-coverage surface functionalization methods are essential for modulating material properties. The limited literature on germanium (Ge) functionalization does not cover SiGe systems. However, the thiol group is generally proposed as the best grafting system for these kinds of substrates. To study functionalization, we synthesized a luminescent model molecule with terminal thiol groups, easily detectable with confocal microscopy. The SiGe substrates are pre-treated with halide passivation (performed using HCl) leaving a Cl-terminated Ge. The substrates are then functionalized with the thiol-based 6-[2,7-bis[5-(5-hexyl-2-thienyl)-2-thienyl]-9-(6-sulfanylhexyl)fluoren-9-yl]hexane-1-thiol molecule. In our work, we show that this process selectively functionalizes the SiGe pattern, where germanium is present, while leaving uncovered the portion of the substrate where only silicon is present. This confirms the selective properties of the functionalization. Here, we optimized conditions for effective SiGe grafting, highlighting the crucial role of oxygen. The study shows that performing the functionalization procedure in an oxygen-free atmosphere significantly enhances the extent of coverage on the substrate, highlighting the importance of an inert environment in achieving optimal functionalization results.