Abstract Mutations in the lysosomal enzyme β-glucocerebrosidase (GCase), which cause Gaucher's disease, are the most frequent genetic risk factor for Parkinson’s disease (PD). Here, we employed global proteomic and single-cell genomic approaches in stable cell lines as well as induced pluripotent stem cell (iPSC)-derived neurons and midbrain organoids to dissect the mechanisms underlying GCase-related neurodegeneration. We demonstrate that a fraction of GCase can be imported from the cytosol into the mitochondria via the translocase of the outer mitochondrial membrane (TOM) import machinery via recognition of internal mitochondrial targeting sequence-like signals. In mitochondria, GCase promotes the assembly and function of mitochondrial complex I (CI). Furthermore, GCase interacts with the mitochondrial quality control proteins HSP60 and LONP1. Disease-associated mutations impair the assembly and function of CI and enhance the interaction with the mitochondrial quality control machinery. These findings reveal a previously unknown function of GCase in mitochondria and suggest that defective CI activity and energy metabolism may drive the pathogenesis of GCase-driven neurodegeneration.