The present study describes the effects of germination on nonnutritional factors and antioxidant activity in the non-conventional legumes Vigna unguiculata (cowpea), Canavalia ensiformis (jack bean), Lablab purpureus (dolichos) and Stizolobium niveum (mucuna). Protease inhibitors and lectins were detected in raw legumes, and were significantly decreased during the germination. Regarding total and individual inositol phosphates (IP5-IP3), important reductions of IP6 and high increases in the rest of inositol phosphates were also detected during this process. In addition, total phenols, catechins and proanthocyanidins increased, accompanied by an overall rise of antioxidant activity (79.6 μmol Trolox/g DW in case of mucuna). Germination has been shown to be a very effective process to reduce nonnutritional factors and increase bioactive phenolic compounds and antioxidant activities of these non-conventional legumes. For this reason, they could be used as ingredients to obtain high-value legume flours for food formulation.