Abstract Accumulating low level mitochondrial insults are thought to be key to aging processes and neurodegeneration. Among other stressors, protein damage due to nitrosative stress negatively impacts mitochondrial function and is linked to neurodegeneration. Using biotin switch technique, we show that mitochondrial proteins are S-nitrosylated not only in the presence but also in the absence of exogenous nitrosative stress. In addition, we revealed a role for the ubiquitin–proteasome system and the outer mitochondrial membrane associated degradation (OMMAD)-component p97 in the quality control of S-nitrosylated mitochondrial. Taken together, constant proteasome-mediated clearance of nitrosatively-damaged proteins from mitochondria is likely important for maintaining organelle function.