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Several studies have shown that nectar-inhabiting bacteria and fungi influence plant and pollinator fitness by modulating their mutualistic interactions. However, little is known about the nectar microbe communities in African agricultural crops, and how visitations by different Afrotropical bee species shape floral nectar microbial community, chemistry, and plant reproductive fitness. In this study, we explored these interactions focusing on Afrotropical pollinator bee species found in Kenya. We found that the stingless bee species Hypotrigona gribodoi and Dactylurina schmidti, and the African savannah honey bee Apis mellifera scutellata introduce only bacteria into the floral nectar of the yellow bell pepper plant Capsicum annum cultivated in a greenhouse, which differed in their volatile emission profiles. Additionally, nectar probing by these bee species shaped the microbiome of C. annum, and significantly affected nectar volume and sugar composition. These findings lay the foundation for further exploration of the microbial influence into plant-pollinator interactions in this country.