Honey bees face escalating threats, notably from floral resource degradation and chronic pesticide exposure. Hive products such as honey and microbial communities in the hive both affect and are affected by bee health. Examining samples from both healthy hives and stressed hives from a single apiary with access to the same floral resources, we profiled the antimicrobial activity and chemical properties of honey and pollen provisions and determined the bacterial and fungal microbiome of the bee gut and the hive environment. Our findings revealed substantial disparities in antimicrobial efficacy, with honey and pollen provisions from healthy hives exhibiting heightened antimicrobial activity against fungal and bacterial hive pathogens. Healthy hives additionally demonstrated increased phenolics and antioxidant content in hive products, with differences in the plant genera of pollen samples suggesting a link to differential foraging behavior. Finally, stressed hives exhibited a more diverse bacterial and fungal microbiome in hive environments, suggesting a diminished capacity to exclude potential pathogens. These results emphasise the need for understanding and proactively managing bee health, as even apparently minor levels of stress can have implications for overall hive fitness as well as the economic potential of hive products.