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This study was conducted at three different locations in South Dakota, USA, to compare the natural (undisturbed) ecosystem (NE) with the tilled (CT) and no-tilled (NT) practices, and to evaluate the tillage effects on soil organic carbon (SOC) and total nitrogen (TN) contents, bulk density (ρb), enzymatic activities and aggregate stability under a corn (Zea mays L.)-soybean (Glycine max L.) cropping system. Results support that NT practices improved soil aggregation as compared to the CT and stored higher SOC and TN concentrations in the aggregates, however, NE treatment outperformed both the tillage systems. Their comparative evaluation with a NE treatment concludes that tilled practices negatively affect soil properties but recommend adoption of NT farming to enhance the soil properties in agroecosystems.