Significance Honey bees pollinate the majority of crops, but their survival is under threat. The bee parasitic mite Varroa destructor is a major cause of honey bee decline. The successful control of Varroa mites depends on a small number of in-hive acaricides. Species-specific activation of the chemical coumaphos is a powerful “pro-drug” approach to attain this selective toxicity and protect bees. We identified a coumaphos-resistant Varroa population that escapes toxicity by down-regulating the activating enzyme, a P450 monooxygenase. Decreased activation is a rare but evolutionarily powerful solution to achieve resistance. It demonstrates that the current proinsecticide approach is under threat, as it can be circumvented, and highlights the need to restart the pipeline to develop selective pest control agents.