The honeybee Apis mellifera plays an invaluable role in pollination and maintaining the world’s ecology. Winter is a grueling season for these fascinating creatures. Population decline in overwintering bees is a persistent threat for beekeepers. During overwintering the honeybees stay inside the hive as it is impossible to acquire nutrition from outside, hence, understanding the effects of winter-diet is imperative. Sugar-water is a prevalent substitute for honey as winter-diet. But this change in diet also results in the change of their gut flora and is thereby linked to diseases like diarrhea and ultimately death. The purpose of this study was to investigate whether a diet where 10 % honey is added to the sugar-water can shift the changes in gut microbiome composition to resemble that of honey-fed overwintering bees. Also, to see if the microbiome composition differs between the ileum and the rectum among the bees on different diets. This was accomplished using Nanopore 16S rRNA sequencing. Compositional difference was observed in the gut flora among bees overwintering to that of sugar-water. This observation is consistent with studies done in the past. A shift towards microbiome flora of bees fed on honey was not observed among bees overwintering on sugar-water complemented with honey. The distinction was more prominent in the rectum as compared to the ileum; it does not seem that the microbiome of the ileum is changing based on diet. Visible morphological changes were also observed in the intestines of the different diet-groups.