Bumblebees are important pollinators for crops and wild flowering plants. Various pesticides have threatened the abundance and diversity of bumblebees. In addition to direct sublethal effects, pesticides may alter the gut microbial communities of bees. Imidacloprid and flupyradifurone insecticides both bind to the nicotinic acetylcholine receptor. However, the latter was assumed to be harmless for honeybees and can even be applied to flowering crops. In this study, we assessed the impacts of these two pesticides on queenless microcolonies and the gut microbiota of Bombus terrestris. We found that 10 μg/L imidacloprid significantly impeded syrup consumption, and postponed the egg-laying period, larvae, and pupae development. It decreased the relative abundance of the bumblebee-specific symbionts, Apibacter and Lactobacillus Firm-5. On the contrary, 10 μg/L flupyradifurone did not reduce syrup consumption, block larvae and pupae development in bumblebees. Although no significant phenotypes were observed, PICRUST revealed that flupyradifurone suppressed pathways, involving carbohydrate metabolism, nucleotide metabolism, translation, and membrane transport. Our findings suggest the appropriate use of this new pesticide may be considered safe for bumblebees, but the underlying mechanism warrants further investigation.