Apis mellifera colonies are a complex, highly organised society that are essential pollinators across the world for both wild flora and cultivated crops. A. mellifera colonies face a myriad of challenges that can be detrimental to their survival – the spread of diseases and pests, poor bee husbandry, loss of essential flora, exposure to commercial insecticides and migratory beekeeping. These daily challenges and exposures have caused a worrying depletion of A. mellifera colonies which is resulting in an increasing concern in the environmental and scientific community. Research is now focused on the relationship honeybee colonies have with the changing environment and the presence of diseases. Female worker honeybees make up the majority of bees within A. mellifera colonies and are essential for hive survival. Worker bees undergo changes to their anatomy and gland secretions as they age to optimise their productivity. Furthermore, worker bees can be divided based on seasons – summer and winter worker bees, both age and seasonality can affect the proteome and therefore the immune response of worker bees. Label-free quantitative (LFQ) proteomics was performed on worker bees at various stages of their lifecycle, between winter and summer, in response to exposure to anti-Varroa treatments and finally in response to the presence of Varroa destructor and Nosema spores within colonies. The work presented in this thesis has identified key age, seasonal, and virus-infected differences within hives at a proteomic level. These results show both age-dependent evolution and environmental adaptions experienced by a hive highlighting their complex relationship and vulnerability to external threats. Importantly, this work has highlighted the impact of anti-Varroa treatments and the potential side effects towards colonies. Finally, work conducted on the effects of Varroa mites and Nosema spores on bees highlighted the need to better understand how these pathogens interact when both are infecting colonies simultaneously. The results presented here provide a novel insight into the proteomic changes that occur in worker bees when exposed to different external factors. However, it also highlights the need for further research into how honeybee workers adapt to stresses such as insecticide exposure and dual infections by Varroa and Nosema.