Organic agroecosystems “rely on ecological processes, biodiversity and cycles adapted to local conditions". Soil health is “the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals, and humans” and can be used to assess agroecosystems. The fertility of organic agroecosystems is dependent upon soil organic matter, an indicator of soil health that supplies much of the nitrogen (N) and carbon (C) in soil. Despite the potential to use soil health as a dynamic measure few data sets compare soil health of different organic systems. My research compares the effects of climate and key best management practices (disturbance, amendment type, and livestock integration) on C sequestration, N cycling and greenhouse gas (GHG) emissions in five organic cropping systems. The data also contribute to our understanding of how microbial community members controlling reactive N (nitrate, nitrous oxide) and C cycling contribute to or reduce GHG as well as the potential of reduced tillage organic systems to lower GHG emissions when N is coupled with C in organic materials. This dissertation research verifies that the types and quantities of N cycling microorganisms can be used as indicators of soil health to assess the impact of short and long-term management on biogeochemical processes (the transformation and cycling of elements between non-living and living matter) that reduce or contribute to global climate change in long-term organic systems. A reduction in GHG emissions benefits the public and may increase the value added of certified organic foods.