Soil nutrient and physical status in small holder farms in southeastern Nigeria are subjected to debilitating effects of continuous cropping without adequate efforts towards replenishment and conservation to ensure sustainability of soil resources. Although inorganic fertilizers are quick acting for soil nutrient enhancement, to guarantee soil health they must be used within the context of integrated soil fertility management relative to soil type and other climatic conditions. On the other hand, apart from maintaining required nutrient levels, the use of appropriate crop combinations and arrangements in farmers' fields can improve soil health. Leguminous plants including tree, shrub and annual species have been determined to be useful components in such systems. These species can contribute immensely to soil carbon and other mineral contents in addition to improving soil physical properties. Apart from their high edible protein content, some leguminous seeds also have high phytate content, which should enhance the bioavailability of Zn, making them good nutrient sources in human and animal nutrition. However, indigenous leguminous tree, shrub, and grain legume species are currently underutilized in the common cropping systems on smallholder farms. While tree species are lost through logging, with very limited research toward their improvement, research on grain legumes has been limited in this zone resulting in the loss of indigenous grain species. Low available soil P is another constraint to legume cultivation in this region that has to be addressed through well coordinated agronomic research. Increased and sustainable food production on small holder farms in southeastern Nigeria is possible with improved practices within the prevailing cropping systems. This is achievable with intensive breeding, agronomic and utilization studies on legume species in the cropping systems.