Abstract To gain a deeper understanding of the molecular basis of pollen foraging preference, we characterized the proteomes of antennae and brains of bees foraging on pear and rapeseed flowers, and the volatile compounds from nectar, anther, and inflorescence of both plants. Bees foraging on the pollen of the two plants have shaped the distinct proteome arsenals in the antenna and brain to drive olfactory and brain function. In antennae, bees foraging on pear (PA) pollen pathways associated with protein metabolism were induced to synthesize new proteins for modulation of synaptic structures via stabilizing and consolidating specific memory traces. Whereas, bees foraging on rapeseed (BA) pollen pathways implicated in energy metabolism were activated to provide metabolic fuels critical for neural activity. These findings suggest that the distinct biochemical route is functionally enhanced to consolidate the divergent olfaction in PA and BA. In brain, although the uniquely induced pathways in bees forging on both plants are likely to cement selective roles in learning and memory, pollen foraging preference in bees is mainly drived by olfaction. Furthermore, both plants have shaped different repertoires of signal odors and food rewards to attract pollinators. The suggested markers are potentially useful for selection of bees to improve their olfaction for better pollination of the plants. Highlights • Pollen foraging preference in bees is regulated by olfaction rather than brain function. • Bees foraging pear and rapeseed flowers develop distinct biochemical route to consolidate divergent olfaction. • Suggested markers are potentially useful for selection of bees to improve their olfaction for better pollination service. [ABSTRACT FROM AUTHOR]