The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.