Mitochondrial proteostasis depends on precise N-terminal processing of imported precursor proteins, and defects in this maturation step are implicated in severe human diseases, yet the functional impact in humans remain unclear. We show that the intermediate cleaving peptidase ICP55, that removes a single amino acid, acts as a key stabiliser of multimeric mitochondrial protein complexes. Using proteomics and complexome profiling, we identify over one hundred human ICP55 substrates and demonstrate that loss of ICP55 triggers proteome-wide destabilisation of protein assemblies, leading to the redistribution of their components into smaller subcomplexes. Our findings uncover a conserved, post-translational mechanism that safeguards mitochondrial proteostasis by regulating complex integrity through a single-amino-acid cleavage and reveal N-terminal proteoform control as an unexpected, novel layer of organellar homeostasis.