The critical metal germanium (Ge) is recovered as a by-product of mining other commodities, such as zinc and thermal coal. We investigated the Ge incorporation mechanism in sphalerite synthesized under hydrothermal conditions like those of sediment-hosted Zn-Pb deposits. Sphalerite ± galena ± barite formed via reactions of Ge ± Fe ± Cu ± Ba-bearing brine with calcite and reduced sulfur at 200 °C and water vapor-saturated pressure. The products were examined using backscattered electron (BSE) imaging, electron probe microanalysis (EPMA), electron backscattered diffraction (EBSD), synchrotron X-ray fluorescence (SXRF) and micro-X-ray absorption near-edge structure (μ-XANES). We show that Ge(IV) is incorporated into sphalerite and bonded with reduced sulfur, both in the experimental sphalerite and in natural zinc ore samples from the MacArthur River Zn-Pb-Ag deposits, Australia. Copper K-edge XANES spectra show that copper occurs as Cu(I) in the experimental sphalerite, consistent with previous studies on Cu in natural sphalerite. The experiments reveal that Ge(IV) substitution in sphalerite occurs with and without the presence of other metal ions (e.g., Cu(I)), indicating that Ge(IV) substitution can be accommodated via charge balance by vacancies as well as by coupled substitution in the synthesized sphalerite. Ab initio quantum chemical simulations confirm that sphalerite can readily accommodate Ge, with the crystal structure and average Zn-S, Zn-Zn, S-S distances retained when replacing > 3 mol% of the Zn sites with Ge(IV), Ge(II), Cu(I) or Fe(II), demonstrating the resilience and flexibility of the sphalerite crystal structure. These Ge incorporation mechanisms explain the previous observations of multiple ways of Ge incorporation in natural sphalerite. The study provides experimental and molecular simulation insights for understanding the processes related to the formation and extraction of Ge in zinc ores.