Honey bees are valuable bioindicators of environmental contamination due to their wide foraging range and exposure to diverse biotic and abiotic stressors. This study evaluates the use of honey bees as bioindicators for detecting per- and polyfluoroalkyl substances (PFASs) in areas with varying levels of exposure risk (high-, intermediate-, and low-), as well as their potential effects on gut-microbial communities. Analytical chemistry to detect PFASs and pesticide residues were combined with molecular and metagenomic analyses to identify common honey bee pathogens and characterize gut-microbial communities. Short-chain PFASs were predominated over long-chain compounds, particularly in high-risk areas, while pesticide residues occurred in only a few apiaries. Molecular analyses revealed several widespread pathogens, while metagenomics showed a stable gut microbiome mainly composed of the genera Lactobacillus, Bartonella, Bombilactobacillus, Snodgrassella, Gilliamella, Bifidobacterium, and Gluconacetobacter. However, microbial-community composition differed significantly between apiaries with high- versus low-risk PFAS exposure. These results support honey bees as effective bioindicators for environmental PFAS monitoring and suggest that PFAS exposure may be associated with alterations in their gut-microbial communities. Further research is needed to elucidate the impact of PFASs on honey bee toxicity, gut-microbiota composition, and overall health.