Honeybees are significant to agriculture and global ecosystems due to their role as key pollinators. The honeybee’s gut microbiota is necessary for maintaining their health, providing nutrition and protection against pathogens. The objective is to develop effective strategies to promote the well-being of honeybee species. This paper comprehensively reviews current literature utilizing advanced genomic techniques to characterize bee gut microbial diversity. It examines culture-independent and culture-dependent methods to classify microorganisms inhabiting the bee gut. Their symbiotic relationships and contributions to critical bee physiological processes are also explored. The gut microbiome holds an indispensable role in bee health by regulating immune function, nutrient absorption and defense against pathogens. Specific bacterial taxa like Lactobacillus, Bifidobacterium, Snodgrassella, Apibacter, Frischella and Gilliamella exhibit probiotic, antimicrobial and symbiotic properties that safeguard bee gut homeostasis. The unique microbial composition of honey, influenced by the bee gut microbiota and environment, holds potential prebiotic and probiotic benefits for human health. Maintaining a balanced bee gut microbiome through microbiome engineering could strengthen bee resistance to diseases, thereby addressing worldwide bee population declines. Further unravelling the health impacts of honey microbes could uncover novel therapeutic applications and advance sustainable apiculture and human nutrition initiatives.