Honey bee (Apis mellifera) queens are failing, and this may be due in part to widespread miticide use by beekeepers. The ectoparasitic mite, Varroa destructor, is a major pest of honeybees and synthetic insecticides are often used to control Varroa. Amitraz is widely used by beekeepers worldwide. Amitraz is thought to be of low toxicity to bees, but applying high doses can cause negative effects. Here, we demonstrate a sublethal dose of amitraz can affect the detoxification, cyclic adenosine monophosphate (cAMP)-dependent protein kinase, immunity, antioxidant capacity, and development of honeybee queens when queens were exposed to amitraz (2.5 ppm) under laboratory conditions. Downregulation of genes related to detoxification enzymes, cAMP-dependent protein kinase, immunity, antioxidant enzymes, and development was observed. Sublethal doses of amitraz had no effects on the viability of spermatozoa stored in spermathecae of queen when treated topically in the laboratory. Lastly, we treated colonies with three formulations of amitraz and followed queens in these colonies for 3 months to explore queen loss and/or other adverse effects of miticide treatment. Queen loss averaged about 30% over all treatment groups including untreated control colonies and no reduction in sperm viability was seen with amitraz treatments when queens remaining after 3 months were dissected. This research demonstrates that chemical exposure can affect some aspects of the queen immune system but sperm viability and queen longevity over 3 months were unaffected by colony level amitraz treatments under real-world conditions in honey bee colonies.