Lewy bodies are neuropathologically associated with Lewy body dementia (LBD), but little is known about why they form or their role in the disease process. We previously reported Lewy bodies are a common feature of older individuals with primary mitochondrial diseases. However, as they are not an invariant finding, understanding differences between those with and without Lewy bodies may provide insights into factors that govern the formation of Lewy bodies in Lewy body disease (LBD). The present study sought to investigate whether deficient mitophagy in the context of mitochondrial dysfunction may underlie Lewy body formation. Post-mortem tissue was obtained from the cingulate gyrus and dorsal motor nucleus of the vagal nerve (DMV) of mitochondrial disease cases with Lewy bodies, primary mitochondrial disease cases without Lewy bodies, and control cases, in addition to LBD cases as comparison. An array of mitophagy and autophagy markers were quantified in 50 individual neurons per cingulate gyrus and all neurons per DMV using immunofluorescent analysis. No significant differences were found between groups, although there was a striking enrichment of markers of autophagic mitochondria and autophagic vesicles within Lewy bodies. Evaluation of diffuse α-synuclein aggregates, thought to precede Lewy body formation, suggested only autophagic mitochondria were present in early aggregates, perhaps suggesting sequestration of dysfunctional mitochondria is an early step in Lewy body formation. To characterise the composition of Lewy bodies, discovery proteomics was performed on isolated insoluble proteins from frozen cingulate gyrus, which identified up-regulation of markers of aggresomes, a regulated cellular response that occurs when protein degradative pathways become overwhelmed, a mechanism of spatial protein quality control (sPQC). Taken together, these findings are consistent with impairment of cellular waste handling pathways in Lewy body-bearing neurons, and that the formation of a Lewy body could be a deliberate cellular response to compartmentalise such waste.