Although organic standards do not refer directly to soil health, organic agriculture has the potential to improve soil health and environmental services by promoting soil conservation and reducing greenhouse gases. This chapter presents findings from a field experiment which continuously monitored the soil health of an organically managed production system from 2003 to 2014. The experiments focus on intensive organic vegetable crop production systems typical of experienced fresh market growers. The research sought to evaluate short- and long-term effects of various different management systems, including crop rotations, cover crops and animal amendments. We discuss the impact of these measures in terms of nutrient release, soil health, greenhouse gas emissions and ecosystem structure and function.