Pollinator decline is one of the gravest challenges facing the world today, and the overuse of pesticides may be among its causes. Here, we studied whether glyphosate, the world's most widely used pesticide, affects the bumblebee gut microbiota. We exposed the bumblebee diet to glyphosate and a glyphosate-based herbicide and quantified the microbiota community shifts using 16S rRNA gene sequencing. Furthermore, we estimated the potential sensitivity of bee gut microbes to glyphosate based on previously reported presence of target enzyme. Glyphosate increased, whereas the glyphosate-based herbicide decreased gut microbiota diversity, indicating that negative effects are attributable to co-formulants. Both glyphosate and the glyphosate-based herbicide treatments significantly decreased the relative abundance of potentially glyphosate-sensitive bacterial species Snodgrasella alvi. However, the relative abundance of potentially glyphosate-sensitive Candidatus Schmidhempelia genera increased in bumblebees treated with glyphosate. Overall, 50% of the bacterial genera detected in the bee gut microbiota were classified as potentially resistant to glyphosate, while 36% were classified as sensitive. Healthy core microbiota have been shown to protect bees from parasite infections, change metabolism, and decrease mortality. Thus, the heavy use of glyphosate-based herbicides may have implications on bees and ecosystems.