Cropping systems in the Northern Great Plains have shifted from fallow-based to legume-based systems. The introduction of grain legumes has impacted soil organisms, including nitrogen fixers, pathogens, mycorrhizae and fauna, and the processes that they perform. These legume seed exudates, rhizosphere exudates, and crop residues impact the soil biotic community. The benefits of legumes in rotation are in part due to the changes occurring in the soil biology. The most widely studied legume-microbial association is dinitrogen fixation which adds plant available nitrogen into the soil system. Many other associations, however, also benefit from the legume in a cropping system. These include, but are not limited to, mycorrhizal associations that improve plant nutrient and water status, changes in the pathogen load and disease development and overall changes in the soil community. The microbial and faunal communities found on legume seeds and roots are different from those found on non legumes. Residue and carbon quality characteristics of the legume alter the soil microbial community too. On the negative side, legumes contribute to nitrous oxide emissions because after the fixed atmospheric N gets nitrified, it faces potential denitrification loss just like fertilizer N. The enhanced microbial activity with legume seed exudates, rhizosphere exudates and crop residues also contribute to carbon dioxide emissions. Therefore, the majority of the attributes of legumes in a cropping system are beneficial, but their contribution to greenhouse gases is a negative effect.