Mitochondrial mass and mitochondrial DNA (mtDNA) copy number are coupled to metabolic demand at the cellular, tissue and organismal level, however, the molecular basis for homeostatic regulation of mtDNA is not understood. Here we show that mitochondria and mtDNA copy number are regulated by compartmentalisation of iron-sulfur (Fe-S) clusters, glutathione and cysteine, a mechanism we exemplify in model systems ranging from plants to human cells. Using genome-wide CRISPR screens we discovered that the mitochondrial ABC-family transporter, ABCB7, is a negative regulator of mtDNA copy number. Partial silencing of ABCB7 in human cells increases mtDNA 2-3 fold, increasing mitochondrial mass and function. ABCB7 silencing engages the cellular iron starvation response whilst simultaneously compelling mitochondrial accumulation and cytosolic depletion of Fe-S clusters, stabilising the mitochondrial glutathione transporter, SLC25A39. Transport of glutathione from the cytosol into mitochondria was co-incident with cytosolic cysteine depletion and mitochondrial cysteine accumulation, which was necessary and sufficient to increase mtDNA copy number in an integrated stress response-dependent fashion, with induction of PGC1β and ERRα to drive mitochondrial gene expression. Silencing or partial loss of function mutations in the ABCB7 homologs of D.melanogaster, S.cerevisiae and A. thaliana elicit similar increases of mtDNA within these organisms. These data reveal a fundamental metabolic logic that couples compartmentalisation of redox co-factors to organellar genome content; a conserved axis across eukaryotes that pre-dates the mtDNA replication machinery.