Mitochondria are critical metabolic organelles for cell health and function. Healthy mitochondria are maintained in our cells through the activity of mitochondrial quality control pathways, and dysfunction of these pathways has been linked to neurodegenerative diseases including Parkinson’s disease. A poorly characterised component of the mitochondrial quality control machinery is the mitochondrial unfolded protein response (UPRmt). The UPRmt is a transcriptional program that boosts the levels of select mitochondrial proteins in response to protein folding stress to help repair the mitochondrial protein folding environment. While we know the UPRmt is activated in response to mitochondrial stress, little is known about how the UPRmt is signalled and how it protects and repairs mitochondrial proteostasis in humans. We have developed a new proteomics framework which enables temporal analysis of mitochondrial proteostasis. We discover that three distinct signalling nodes regulate UPRmt activity. Each node of the UPRmt plays critical overlapping roles in protecting mitochondrial proteostasis, but the protection is achieved by each node through unique transcriptional programs. We also find that the UPRmt functions across two phases of mitochondrial stress which include an acute stress phase, and a repair and recovery phase. Protection of mitochondria across both phases is essential for mitochondrial metabolism, including oxidative phosphorylation. Taken together, our proteomics framework has revealed how three separate UPRmt signalling nodes converge to help keep mitochondria healthy and provides insights into how dysfunction of the UPRmt can contribute to disease development.