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Protein quality control is essential for maintaining mitochondrial fidelity. Proteins damaged by reactive oxygen species necessitate quality control to prevent mitochondrial dysfunction connected to aging and neurodegeneration. Here we report a role for the AAA ATPase p97/VCP and the proteasome in the quality control of oxidized mitochondrial proteins under low oxidative stress as well as normal conditions. Proteasomal inhibition and blocking p97-dependent protein retrotranslocation interfered with degradation of oxidized mitochondrial proteins. Thus, ubiquitin-dependent, p97-, and proteasome-mediated degradation of oxidatively damaged proteins plays a key role in maintaining mitochondrial fidelity and is likely an important defense mechanism against aging and neurodegeneration.