There has been an increasing interest in evaluating the health of soil resources motivated by the growing cognizance that soil is a critically important component of the earth’s biosphere, playing an important functional role not only in producing food and fibre, but also in maintaining ecosystem services and global environmental quality. There was a great deal of concern in developing management practices that improve the capacity of the soil to perform its various functions by identifying the physical, chemical and biological soil attributes and by quantifying the changes in the state of soil resulting from different agronomic practices. The goal of this chapter is to discuss the effects of crop rotation and intercropping management practices that are relevant to productivity and their impact on soil health enhancement and stability. This chapter will also attempt to contribute holistic appreciations of the importance of leguminous crops and soil organic matter in maintaining healthy soils, sustaining crop productivity and enhancing biodiversity.