Use of high tunnel crop production is expected to increase to meet the growing demand for locally produced fresh market vegetables. These structures have the potential to offer many production benefits; however, managing soil quality in these structures is challenging and work in the area is limited. In this 3-year study, we compared the impacts of organic and inorganic fertility amendments on soil quality, nutrient availability, and the productivity of chard (Beta vulgaris L.) and sweet peppers (Capsicum annuum L.) produced in high tunnel and open field systems. Fertility amendments included a green manure treatment [hairy vetch (Vicia villosa Roth) and dehydrated alfalfa meal], partially composted and pelletized chicken litter, urea, and an unfertilized control. Chard was grown in 2011, and peppers were grown in 2012 and 2013. Soil nutrients, microbial activity, active carbon, pH, electrical conductivity (EC), total soil organic matter, and yield were quantified. Chard yield was lower in the high tunnel compared with the open field in 2011, but pepper yield was greater in the high tunnel in 2012 and 2013. Productivity of chard was lower in the green manure compared with urea in 2011 across high tunnel and open field production systems, but no difference in pepper yield was observed between plants receiving fertility inputs in either 2012 or 2013. Repeated application of green manure and chicken litter resulted in soils with increased microbial activity and active carbon, but the green manure was the only treatment successful at accruing carbon in the high tunnel over time. High tunnel production resulted in greater EC compared with the open field, but levels were not considered inhibitory for chard or peppers. High tunnels can increase vegetable crop productivity in the midwest United States, and organic fertility amendments can improve soil quality as measured by soil microbial activity and active carbon in high tunnel and open field production systems.