Fruits and vegetables are subjected to a number of preparation processes to improve their digestibility, sensory properties and extend their shelf-life. Thermal and ultrasonic treatments are often used in the production of various fruit and vegetable based products that may contain allergenic proteins. Therefore, it is important to investigate the impact of these technologies on their allergenicity in order to provide ways of managing allergy risks during production and to explore new technologies aimed at reducing the allergic potential of the final product. The aim of this study was to investigate the effect of ultrasound and heat treatment on the in vitro immunoreactivity of protein extracts of fruits and vegetables (apple, eggplant, fennel). Based on the extensive statistical analysis of the archived FABER assays of 111 individuals, sera of three patients with high levels of specific immunoglobulin E for allergenic apples, eggplants and fennel were selected for further studies. After ultrasonic and thermal treatment, protein extracts were analyzed by SDS-polyacrylamide gel electrophoresis and immunochemical methods Western blot and ELISA. The results of the study showed that ultrasonic and thermal treatment altered the properties and allergenicity of fennel, eggplant and apple proteins. Due to the cross-reactivity with peach antigens, fennel treatment by ultrasound or heat could prevent additional allergic reactions in people allergic to peach. In order to gain more insight into the effects of different treatments and the variety of individual allergic responses, a larger number of subjects need to be analyzed. The results of this study increase the understanding of the impact of conventional as well as novel processing methods on fruit and vegetable allergens.