Pollinator health depends critically on gut microbiome composition, yet species-specific responses to agricultural environments remain unclear. We compared gut microbiome dynamics and dietary shifts in Osmia excavata, Megachile rotundata, and Apis cerana during alfalfa pollination using 16S rRNA sequencing and rbcL metabarcoding. Alpha diversity revealed distinct patterns: O. excavata showed reduced richness but increased evenness after foraging, M. rotundata exhibited reduced diversity, while A. cerana remained stable. Beta diversity demonstrated microbiome convergence among species after release, indicating environmental filtering. Dietary analysis revealed polylectic foraging dominated by Citrullus lanatus, Peganum nigellastrum, and Zea mays, with minimal alfalfa consumption. Pseudomonadota and Bacillota predominated, with species-specific signatures: Gilliamella in A. cerana, Lactobacillus in M. rotundata, and Bacillus in O. excavata. These findings demonstrate that microbiome assembly reflects host sociality–environment interactions, with solitary bees showing greater plasticity. This study provides a microbial foundation for pollinator conservation in agricultural systems.