Mitochondria are essential organelles that provide the energy to power most biochemical reactions in our cells. Dysfunctional mitochondria have been implicated in the pathology of many diseases from cancer to diabetes, while defects in quality control pathways that maintain mitochondrial health can cause Parkinson’s disease. One major mitochondrial quality control pathway is the mitochondrial unfolded protein response (mtUPR). The mtUPR is a transcriptional program that responds to mild mitochondrial damage by inducing the expression of proteins that boost both mitochondrial health and cellular function. Using a small molecule inhibitor of mitochondrial HSP90 to induce protein aggregation within mitochondria, we have shown that the mammalian mtUPR consists of three separate signalling arms mediated by the transcription factors CHOP, ATF4 and ATF5. CRISPR/Cas9 knockouts of these three transcription factors revealed that each arm of the mammalian mtUPR functions in a non-redundant manner. To understand how each transcription factor contributes to the folding state of the mitochondrial proteome during stress, we have characterised the mitochondrial stress ‘aggresome’. Comparative analysis of the mitochondrial aggresome in CHOP, ATF4 and ATF5 knockout lines has revealed at a functional level how each signalling arm of the mammalian mtUPR promotes mitochondrial repair.