Gut microbiome disequilibrium is increasingly implicated in host fitness reductions, including for the economically important and disease‐challenged western honey bee Apis mellifera. In laboratory experiments, the antibiotic tetracycline, which is used to prevent American Foulbrood Disease in countries including the US, elevates honey bee mortality by disturbing the microbiome. It is unclear, however, how elevated individual mortality affects colony‐level fitness.We used an agent‐based model (BEEHAVE) and empirical data to assess colony‐level effects of antibiotic‐induced worker bee mortality, by measuring colony size. We investigated the relationship between the duration that the antibiotic‐induced mortality probability is imposed for and colony size.We found that when simulating antibiotic‐induced mortality of worker bees from just 60 days per year, up to a permanent effect, the colony is reduced such that tetracycline treatment would not meet the European Food Safety Authority's (EFSA) honey bee protection goals. When antibiotic mortality was imposed for the hypothetical minimal exposure time, which assumes that antibiotics only impact the bee's fitness during the recommended treatment period of 15 days in both spring and autumn, the colony fitness reduction was only marginally under the EFSA's threshold. Synthesis and Applications. Modelling colony‐level impacts of antibiotic treatment shows that individual honey bee worker mortality can lead to colony mortality. To assess the full impact, the persistence of antibiotic‐induced mortality in honey bees must be determined experimentally, in vivo. We caution that as the domestication of new insect species increases, maintaining healthy gut microbiomes is of paramount importance to insect health and commercial productivity. The recommendation from this work is to limit prophylactic use of antibiotics and to not exceed recommended treatment strategies for domesticated insects. This is especially important for highly social insects as excess antibiotic use will likely decrease colony growth and an increase in colony mortality.