The consumption of seeds of the Fabaceae family is distributed worldwide mainly due to the high content in proteins, carbohydrates, dietary fiber and polyunsaturated fatty acids, jointly with vitamins and minerals. However, they contain several non-nutritive compounds (NNCs) that can exert adverse or beneficial actions upon ingestion depending on their chemical structure, concentration, time of exposure and their interaction with other dietary components. In this review, we present the representative legume NNCs, their chemical nature and their adverse and beneficial biological actions. Moreover, we summarized updated findings on the effect of different traditional processing, taking in mind that legumes are mainly consumed in the household milieu, on the concentration of legume NNCs. The results of the in-vivo studies prove that the reduction/elimination of legume NNCs improve nutritional quality and the fate of improvements depends on many parameters such as botanical source, chemical composition, content, type of processing and operational conditions used, among others. Together, this review can provide a comprehensive perspective for further elucidating the roles of plant lectins that may target programmed cell death pathways. This review may, in turn, ultimately help to consumers in which legumes are part of a vegetarian diet or are consumed as staple food which must take into consideration the improvement of legume nutritive quality by traditional processing.