Pollen allergies affect a large proportion of the global population, and preexisting conditions such as asthma increase susceptibility and symptom severity. Due to its microscopic size and prevalence, pollen is difficult to avoid, particularly in spring —the primary reproductive period for many plants. Remediation is further complicated by pollen’s reproductive functions. Beyond acting as a vehicle for the transfer of male genetic information, pollen proteins, or allergens, perform key, non-allergenic roles, including supporting male gamete development, facilitating pollen-stigma recognition, driving metabolic processes in pollen tube growth, and contributing to plant immune responses. Consequently, removing allergen genes risks damaging plant health and fertility. This study proposes a synthetic biology based approach to selectively reduce pollen allergenicity while maintaining its reproductive functions. We targeted a birch tree allergen, Betula verrucosa allergen 1 (Bet v 1), which binds to Immunoglobulin E (IgE) antibodies in mucosal tissues and skin, triggering histamine release. Our approach involves modifying a key IgE-recognized epitope in Bet v 1 while maintaining its physiological role in birch trees. Using Agrobacterium-mediated transformation, a mutated Bet v 1 gene and a CRISPR-Cas9 structure designed to silence the allergenic allele may be introduced into birch tissue cultures through deactivated tumor-inducing (Ti) plasmids in Agrobacterium. This approach enables the production of hypoallergenic birch trees with preserved reproductive and physiological functions. Moreover, this approach offers a model for broader remediation of other pollen-producing species.