<p>Like many agricultural animal systems, common apiculture (honey bees) practice has led to a reliance on chemical treatments to mitigate parasites and diseases. These agrichemicals typically take the form of acaracides (e.g., amitraz) and antibiotics (e.g., oxytetracycline; OTC), both of which can persist in various hive matrices and have unforeseen effects on colony health, such as the evolution of resistance by disease agents or decreased reproductive fertility of the bees themselves. The honey bee microbiome is a critical component of the food-processing and pathogen response of honey bees and has been shown to be impacted by agrichemicals, although the bulk of the research has been on honey bee workers, rather than the queen, which is commonly the sole reproductive of the colony, possesses her own distinct microbiome, and is strongly buffered from the external environment by alloparental care from the workers. Over the course of three experiments, we exposed queens to amitraz, OTC, or control in an industry-standard apiary. Queens were assessed for morphological, reproductive, and microbiome traits, and male and female brood were assessed for survival to pupation. We found that amitraz negatively impacts the viability of stored sperm in queens (from 87.3 ± 8.9% to 65.4 ± 7.5%) but not egg laying or brood survival. OTC disrupts the microbiome community in queens, altering community composition, but not alpha diversity. In these studies, microbial and reproductive phenotypes appear to be unrelated, suggesting a more nuanced relationship between the honey bee queen microbiome and overall colony social organization.</p>