Lupin is peanut's closest relative amongst foods and it has been estimated that approximately 50% of individuals with peanut allergy can react to lupin. Thus the addition of lupin to flour was soon followed by reports of allergic reactions to this hidden and generally unlabelled allergen. In France, the first report of lupin anaphylaxis was in 1999 but by 2002, lupin was the fourth most frequent cause of severe food-associated anaphylaxis reported to the French Allergy Vigilance Network. However, although most cases have involved individuals allergic to peanut, there is at least one report of an individual allergic to lupin and some legumes (chickpea, lentil and white beans) who could tolerate peanut. The reported symptoms of allergic individuals after eating lupin include oral itching and urticaria (hives) and angioedema (wheals) of the skin as well as more severe symptoms (anaphylaxis). Several cases have included acute asthma or breathing difficulty due to throat swelling.

It has been suggested that in future lupin should be added to the list of food ingredients that must be labelled.