Mutations in the GBA gene encoding glucocerebrosidase cause Gaucher disease (GD), the most prevalent of the lysosomal storage disorders (LSDs) and increase susceptibility to Parkinson disease (PD). Clinically the two disorders can present in a similar manner with analogous pathological features, suggesting mechanistic links between the two disease states. An increasing body of evidence implicates defects in quality control pathways in both, and suggests that LSDs, as a group, can be classed as disorders of autophagy. Using a mouse model of type II neuronopathic GD, we observed global defects in cellular quality control pathways in midbrain neurons and astrocytes. Our data suggest that downregulation of autophagy, mitophagy, and the ubiquitin-proteasome system (UPS) results in accumulation of dysfunctional and fragmented mitochondria, insoluble SNCA/α-synuclein deposits and ubiquitinated proteins. These observations show that dysfunction of cellular quality control pathways lead to impaired energy and free radical homeostasis, providing new insights into the mechanisms of neurodegeneration in GD and illuminating the links between GD and PD.