Varroa destructor is an ectoparasitic mite and is considered one of the most important causes of honey bee population loss. In the last years, substances of botanical origin have emerged as natural alternatives to diminish the mite population levels. Propolis is a natural product and is used by honey bees for multiple tasks, including protection from pathogens and parasites, and varroacidal activity of propolis extracts has been shown. In this study, we investigated the potential of propolis, collected by native Algerian honey bee subspecies (Apis mellifera intermissa and A. m. sahariensis) in different locations in Algeria and extracted by ultrasound, to control mites of V. destructor and tested the safety for the honey bees. The most important results were that the best propolis extracts at 10% killed 100% of the Varroa mites within 3–4 h in a Petri dish assay. In addition, when we sprayed A. m. intermissa bees infested with Varroa mites with a 10% concentration in a mini-hive setup, we scored a high mite mortality of 85–87% with the best propolis extracts, and importantly, there was no mortality in the bees. Our data demonstrated that propolis extracts in Algeria could be used in honey bee colonies by spraying against Varroa mite infestations, which may develop as an easy method for local beekeepers to control Varroa in their hives. Further research should investigate the mechanism of action.