Serious allergic reactions are increasing globally. Within this context, fatal anaphylaxis from hazelnut allergies is a critical public health concern. Hazelnuts, which are a common ingredient of many foods, contain many proteins that cause severe allergic reactions. Hazelnuts from all of the major commercial growing locations worldwide contained Spirosoma pollinicola sp. proteins. This endotoxin‐producing bacterium is linked to the allergenicity of hazelnut pollen. We were unable to remove the contamination by S. pollinicola proteins, showing that this bacterium is a seed endosymbiont. Comparative proteomics revealed significant variations in the allergenic protein composition of nuts that correlated with patient immune responses. Hazelnuts from provenances 17 and 18 exhibited lower levels of key antigens, particularly Cor a 9 and Cor a 14, highlighting their potential as candidates for genetic modification to mitigate allergenicity. Moreover, Spirosoma protein persistence may influence hazelnut allergenicity and the patient's immune response