During and after the pollen season, an increase in food-triggered allergic symptoms has been observed in pollen-food syndrome patients, possibly due to seasonal boosting of pollen-IgE levels. It has been suggested that consumption of birch-pollen-related foods plays a role in seasonal allergenic inflammation. However, whether this increased pollen sensitization during the pollen season can also affect the allergenicity of allergens that are non-cross-reactive with birch pollen remains in question. This study presents the case of a patient with soy allergy and pollinosis, who experiences worsening of gastrointestinal (GI) symptoms during the birch pollen season even though the eliciting food factor does not cross-react with birch pollen allergens and their homologs (e.g., Bet v 1 and Gly m 4). The results showed a notable increase in sIgE for Gly m 4 (3.3 fold) and Bet v 1 (2.6 fold) during the birch pollen season compared to outside the birch pollen season, while Gly m 5 and Gly m 6 showed only a slight increase (1.5 fold). The basophil activation test (BAT) showed that in this patient Gly m 5 and Gly m 6 are clinically relevant soy allergens, which correlates with the reported clinical symptoms to processed soy. Moreover, the BAT against raw soy shows an increase in basophil activation during the birch pollen season and a negative basophil activation result outside the birch pollen season. Thus, the worsening of GI symptoms could possibly be due to an increase in IgE receptors, an over-reactive immune system, and/or significant intestinal allergic inflammation. This case highlights the importance of including allergens that do not cross-react with birch pollen and using a functional assay such as the BAT to evaluate clinical relevance when assessing birch pollen seasonal influence on soy allergenicity.