Complex I (NADH dehydrogenase) is the primary and largest complex of the mitochondrial electron transfer chain required for ATP production. In plants, complex I consists of 47 distinct subunits, with 38 nuclear and 9 mitochondrial encoded. The abundance of complex I is regulated by gene expression, translation, protein import, assembly, and breakdown. Previous studies have examined these processes in detail with the exception of breakdown and as the first site of electron transfer, complex I is prone to oxidative damage requiring regulated proteolysis and turnover. Here, using both genetic and biochemical approaches, we decipher the mechanism by which FTSH3 (Filamentous Temperature Sensitive H3) protease mediates complex I abundance. This is achieved through a direct interaction with the complex I Q-module domain subunit PSST, where the PSST N-terminal residue S70 and the FTSH3 ATPase residue P415 contributes to their interaction. It is the unfoldase activity of FTSH3 that is required to recognise PSST for removal, as this interaction occurs with a proteolytically inactive FTSH3. The interaction of FTSH3 and PSST mediates the disassembly of the matrix arm domain module of complex I resulting in the proteolysis and turnover of matrix arm domain subunits as a means of protein quality control.