Although Varroa destructor is the most serious ecto-parasite to the honeybee, Apis mellifera L., some honeybee populations such as Apis mellifera scutellata in Kenya can survive mite infestations without treatment. Previously, we reported that grooming behaviour could be a potential tolerant mechanism expressed by this honeybee subspecies towards mite infestation. However, both hygienic and grooming behaviours could not explain the lower mite-infestation levels recorded in these colonies. Here, we investigated the involvement of other potential resistant mechanisms including suppression of mite reproduction in worker brood cells of A. m. scutellata to explain the low mite numbers in their colonies. High infertility rates (26–27%) and percentages of unmated female offspring (39–58%) as well as low fecundity (1.7–2.2, average offspring produced) were identified as key parameters that seem to interact with one another during different seasons to suppress mite reproduction in A. m. scutellata colonies. We also identified offspring mortality in both sexes and absence of male offspring as key factors accounting for the low numbers of mated daughter mites produced in A. m. scutellata colonies. These results suggest that reduced mite reproductive success could explain the slow mite population growth in A. m. scutellata colonies.