Controlling populations of varroa mites is crucial for the survival of the beekeeping industry. Many treatments exist, and all are designed to kill mites on adult bees. Because the majority of mites are found under capped brood, most treatments are designed to deliver active ingredients over an extended period to control mites on adult bees, as developing bees and mites emerge. In this study, a 17-h application of 50% formic acid effectively killed mites in capped worker brood and on adult bees without harming queens or uncapped brood. Neither acetic acid nor a combined treatment of formic and acetic acids applied to the West Virginia formic acid fumigator was as effective as formic acid alone in controlling varroa mites. In addition, none of the treatments tested in late summer had an effect on the late-season prevalence of deformed wing virus. The short-term formic acid treatment killed >60% of varroa mites in capped worker brood; thus, it is a promising tool for beekeepers, especially when such treatments are necessary during the nectar flow.