Bee pollen is consumed for its nutritional and pharmacological benefits, but it also contains hazardous allergens which have not been identified. Here, we identified two potential allergens, glutaredoxin and oleosin-B2, in Brassica napus bee pollen using mass spectrometry-based proteomics analyses, and used bioinformatics to predict their antigenic epitopes. Comparison of fermented (by Saccharomyces cerevisiae) and unfermented bee pollen samples indicated that glutaredoxin and oleosin-B2 contents were significantly decreased following fermentation, while the contents of their major constituent oligopeptides and amino acids were significantly increased based on metabolomics analyses. Immunoblot analysis indicated that the IgE-binding affinity with extracted bee pollen proteins was also significantly decreased after fermentation, suggesting a reduction in the allergenicity of fermented bee pollen. Furthermore, fermentation apparently promoted the biosynthesis of L-valine, L-isoleucine, L-tryptophan, and L-phenylalanine, as well as their precursors or intermediates. Thus, fermentation could potentially alleviate allergenicity, while also positively affecting nutritional properties of B. napus bee pollen. Our findings might provide a scientific foundation for improving the safety of bee pollen products to facilitate its wider application.