The consumption of legumes has been linked to several health-promoting effects, mediated by the action of bioactive secondary metabolites (such as prenylated isoflavonoids and stilbenoids). To enhance the production of bioactive compounds, legume seeds were germinated under stress. Fungus appeared to be a more effective stress factor than light and wounding. Moreover, the combination of fungus and light was more promising than the combination of fungus and wounding. The inducibility of secondary metabolites in different legume seeds varied. In terms of total quantity, soybean, kidney bean, lupine and peanut were more promising than mung bean, lablab and winged bean. Also, the type of fungus might affect the bioactive compounds induced, which was suggested to be associated with the distinctive abilities of fungi to metabolize them.