Allergen analysis is central to implementing and monitoring food allergen risk assessment and management processes by the food industry but current methods for determination of allergens in foods give highly variable results. The EU-funded iFAAM project has been working to address gaps in knowledge regarding food allergen management and analysis, including the development of novel mass spectrometry (MS) and immuno -based allergen determination methods. Common allergenic food ingredients (peanut, hazelnut, walnut, cow’s milk and hen’s egg) and common food matrices (chocolate dessert and cookie) have been used for both clinical studies and analytical method development to ensure that the new methods are clinically relevant. Allergen molecules have been used as analytical targets and allergenic ingredients incurred into matrices at levels close to reference doses that may trigger the use of precautionary allergen labelling. An inter-laboratory method comparison has been undertaken for the determination of peanut in chocolate dessert using MS and immuno-based methods. The iFAAM approach has highlighted the need for methods to report test results in allergenic protein. This will allow food business operators to use them in risk assessments which are founded on clinical study data where protein has been used as a measure of allergenic potency.