Food legumes are rich source of dietary proteins, calories, folates, vitamins, minerals and fibre contents. With very low fat and considerable proportion of slowly digestible starch, food legumes are highly beneficial for human health. In recent years, research on the active presence of many bioactive compounds like glycosides, tannins, saponins and alkaloids in legume seeds increased the importance of this group of crops from biomedical point of view. However, some of these if consumed over a threshold quantity for prolonged period may behave toxic, unpalatable or indigestible, and these molecules are collectively known as 'anti-nutritional factors' (ANFs). Enhancing nutrition status and reducing ANFs among food legumes can be achieved through genetic manipulation utilising natural intra- or interspecific variation within a breeding population or any mutant population or by engineering respective biosynthetic pathways. It is important to mention that ANFs have certain role to play in plant metabolism and physiology. Therefore, breeding for high nutrient and low or null ANFs may require close attention to the overall plant physiology or agronomic performance or any other biological implication. © Springer Nature Switzerland AG 2021. All rights reserved.