Germanium (Ge) is a critical raw material used in high-technology industry (i.e., optical industry) applications, and it is predominantly concentrated in coals and Zn-rich deposits. Previous studies on Zn-rich deposits have documented a correlation between Ge enrichment and the Cu, Ag, and/or Pb-Mn contents in the sphalerite crystal lattice. In this study, we observed Ge-rich nanoparticles hosted in Cu-poor sphalerite from the Banbianjie Zn-Ge deposit (>800 t graded at ∼100 ppm Ge), located in southwest China. Laser-ablation−inductively coupled plasma−mass spectroscopy (LA-ICP-MS) analyses revealed that sphalerite contains very heterogeneous Ge contents (172−1553 ppm). Germanium contents showed positive correlations with Fe, Mn, and Pb contents and negative correlations with Cd contents. Higher Ge contents were detected in the darker zones, whereas the lighter zones showed systematically low Ge contents and were enriched in Cd. Using transmission electron microscopy (TEM), Zn-Ge-Pb-S nanoparticles were identified in the darker zones of sphalerite. These nanoparticles exhibited Ge/Pb ratios (0.48−1.96) very similar to those measured in sphalerite (0.36−2.04), suggesting that Ge could be essentially hosted within the nanoparticles. We propose that the amounts of Zn-Ge-Pb-S nanoparticles are related to a self-organization model induced by rapid crystal growth. This self-organization processes may control the fluctuations of element concentrations in the boundary layer. This study highlights the importance of studying the nanoscale expression of critical elements to understand their incorporation mechanisms into natural materials.