SummaryThe extreme resistance of Saccharomyces cerevisiae to copper is overcome by 2‐(6‐benzyl‐2‐pyridyl)quinazoline (BPQ), providing a chemical‐biology tool which has been exploited in two lines of discovery. First, BPQ is shown to form a red (BPQ)2Cu(I) complex and promote Ctr1‐independent copper‐accumulation in whole cells and in mitochondria isolated from treated cells. Multiple phenotypes, including loss of aconitase activity, are consistent with copper‐BPQ mediated damage to mitochondrial iron–sulphur clusters. Thus, a biochemical basis of copper‐toxicity in S. cerevisiae is analogous to other organisms. Second, iron regulons controlled by Aft1/2, Cth2 and Yap5 that respond to mitochondrial iron–sulphur cluster status are modulated by copper‐BPQ causing iron hyper‐accumulation via upregulated iron‐import. Comparison of copper‐BPQ treated, untreated and copper‐only treated wild‐type and fra2Δ by RNA‐seq has uncovered a new candidate Aft1 target‐gene (LSO1) and paralogous non‐target (LSO2), plus nine putative Cth2 target‐transcripts. Two lines of evidence confirm that Fra2 dominates basal repression of the Aft1/2 regulons in iron‐replete cultures. Fra2‐independent control of these regulons is also observed but CTH2 itself appears to be atypically Fra2‐dependent. However, control of Cth2‐target transcripts which is independent of CTH2 transcript abundance or of Fra2, is also quantified. Use of copper‐BPQ supports a substantial contribution of metabolite repression to iron‐regulation.