The presence of undeclared allergens in food products poses a serious health risk to consumers and results in important economic losses for the food industry. The detection of allergens is typically performed using immunological methods. DNA-based methods complement immunoassays and provide higher specificity and sensitivity, especially in processed foods. DNA-based identification of allergens can currently only be performed using well equipped laboratories which can be difficult to implement in an industry settings where the identification should be fast and on-site. In SafeFood, I will develop a protocol to implement cutting-edge Nanopore sequencing technology for rapid, portable identification of allergenic plant ingredients in complex, multi-ingredient food products. DNA-based identification of allergenic plant species has been challenging due to the lack of variation of the traditional DNA barcodes. I will implement more robust species identification methods based on whole plastid genomes. First, I will compile a comprehensive open-access database of allergen species’ plastomes. Then, DNA extraction and library preparation will be optimized for an on-site protocol tailored to the constraints of the food industry. I will create artificial mixtures of complex food, with varying concentrations of allergens to test the method’s sensitivity, specificity and repeatability and compare the results to those of immunoassays. This innovative solution will solve an industry challenge by allowing on-site, fast and accurate allergen identification. By being hosted at a leading DNA service company, BaseClear, and with the collaboration of a specialised academic partner in EU food safety analyses, RIKILT, I will apply my expertise in plant genomics, develop skills in food chain analyses, in R&D and entrepreneurship. At the completion of this fellowship, I will be able to apply this knowledge and skill to further address societal challenges in the food industry.