Mandatory labelling of allergenic food ingredients has helped allergic consumer manage their condition, but unintended allergens and precautionary allergen labels (PAL) continue to cause confusion for allergic consumers and the food industry alike. Identifying doses of food protein that are safe for the majority of allergic consumers and test methods for their analysis are essential for evidence‐based application of allergen labelling. The ThRAll project addressed this by developing a multiplex prototype mass spectrometry (MS)‐based reference method capable of analyzing six allergenic foods (cow's milk, hen's egg, peanut, hazelnut, almond and soybean) with complementary assessment of immunoassay and DNA‐based methods. The MS method was transferable between laboratories and has the sensitivity required to quantify the allergens from egg, milk, almond and hazelnut in chocolate, meeting test method performance requirements identified for these allergenic foods by the recent FAO‐WHO expert consultation. Further refinement is needed to improved sensitivity for peanut and soy. In parallel an approach for harmonizing and integrating oral food challenge data in allergic subjects was developed and data collection piloted using an on‐line database. Data gaps were identified for many allergenic foods and there is an urgent need to confirm the allergenic activity of highly processed food matrices.