► Long term changes in soil quality and crop productivity with fertilizer and tillage. ► Soil Quality Index (SQI) developed using Principal Components Approach. ► Improved soil quality in No-till, Reduced Input compared to conventional management. ► Conservation management improves nutrient availability, soil stability and structure. ► Soil quality concord with microbial nitrogen processing, nitrogen use and leaching. Intensively cropped agricultural production systems should be managed to improve soil quality and ecological processes and ultimately strengthen system capacity for sustained biological productivity. We examined the long-term changes (>20 years) in soil quality and productivity with incorporation of ecological management principles in a set of intensively managed row crop systems of the upper Midwest, USA. Replicated experimental treatments include corn (maize)–soybean–wheat cropping systems under four different management regimes: (a) conventional tillage and fertilizer/chemical inputs ( Conventional), (b) no tillage with conventional fertilizer/chemical inputs ( No-till), (c) conventional tillage with ∼30% of conventional fertilizer/chemical inputs and a leguminous cover crop ( Reduced Input), and (d) conventional tillage with no fertilizer/chemical input and a leguminous cover crop ( Organic). Effects of these treatments on soils were compared by developing a soil quality index (SQI) from 19 selected soil health indicators. An old field community maintained in early succession provided a benchmark for comparison. Reduction in tillage or fertilizer ( No-till, Reduced Input and Organic) resulted in increased SQI and improved crop production. The No-till (SQI = 1.02) and Reduced Input (SQI = 1.01) systems outperformed Conventional management (SQI = 0.92) in nitrogen availability and use efficiency, soil stability and structure improvement, and microbial nitrogen processing. Improvements in soil quality corresponded with increased primary production and crop yield in these systems, illustrating the value of an ecologically defined SQI for assessing the long-term effects of fertility and tillage management regimes in agricultural production systems.