Cacao farmers have struggled to control witches’ broom disease, a fungal infection caused by Moniliophthora perniciosa, because the fungus survives even high doses of strobilurin fungicides. This study reveals how the fungus adapts to the fungicide by switching its metabolism to use alternative energy sources, activating detoxification systems, and using an alternative respiratory pathway. Researchers also discovered that prolonged fungicide exposure can create even more resistant mutants with mutations in genes that control fungal growth and gene expression.