Acreage devoted to low-input and organic vegetable production is increasing rapidly in the Midwestern region due to steady rise in consumer demand. Vegetable growers are increasingly using high tunnels to help meet this demand because they can aid in season extension. However, the long-term soil quality impacts of these structures are unclear. Further, nutrient sources and environmental conditions have potential to modify the cycling of nitrogen, altering availability for plants and loss to the environment, but these dynamics are not well understood in Midwestern vegetable production systems. The objective of this project was to determine the long-term impacts of fertility practices on common indicators of soil, the soil nitrogen cycle, and plant productivity. Over three growing seasons (2011-2013), repeated applications of composted chicken manure and a green manure (hairy vetch) were compared to a conventional fertility treatment and an unamended control in open field and high tunnel settings. Seasonal soil samples were collected to determine treatment impacts on common indicators of soil quality, nitrification and denitrification potential, and the abundance and diversity of nitrogen cycling genes. Sweet peppers were grown to determine treatment effects on plant productivity and act as a biological indicator of nitrogen availability. Results to date indicate that crop nutrient requirements were being met following prolonged use of either organic or conventional fertilizers. However, comparison of indicators of soil quality showed treatment specific variance which varied between the plot locations. On-going analyses are being conducted to quantify treatment impacts on functional transformations and microbial community dynamics connected to nitrogen cycling. This project will identify key ecological processes that are responsible for maintaining crop productivity as well as those contributing to the health of the environment. Understanding how organic and conventional fertility management practices influence agroecosystem processes will lead to more effective and responsible use of fertilizers.