The Conservation Effects Assessment Project (CEAP). was initiated in 2002 to quantify the potential benefits of conservation management practices throughout the nation. Within the Central Claypan Region of Missouri, the Salt River Basin was selected as a benchmark watershed for soil and water quality assessments. This study focuses on two objectives: (1) assessing soil quality for 15 different annual cropping and perennial vegetation systems typically employed in this region, and (2) evaluating relationships among multiple measured soil quality indicators (SQIs). Management practices included annual versus perennial vegetation, and varying grass species composition (cool-season versus warm-season), tillage intensity (no-till versus mulch-till), biomass removal, rotation phase, crop rotation (corn [Zea mays L.]-soybean [Glycine max L. Merr] versus corn-soybean-wheat [Triticum aestivum L.]) and incorporation of cover crops into the rotation. Soil samples were obtained in 2008 from 0 to 5 cm (0 to 2 in) and 5 to 15 cm (2 to 6 in) depth layers. Ten biological, physical, chemical, and nutrient SQIs were measured and scored using the Soil Management Assessment Framework (SMAF). Across SQIs, biological and physical indicators were the most sensitive to management effects, reflecting significant differences in organic carbon (C), mineralizable nitrogen (N), beta-glucosidase, and bulk density. In the 0 to 5 cm layer, perennial systems demonstrated the greatest SMAF scores, ranging from 93% to 97% of the soil's inherent potential. Scores for annual cropping systems ranged from 78% to 92%: diversified no-till, corn soybean wheat rotation with cover crops (92%) > no-till, corn-soybean rotation without cover crops (88%) > mulch-till corn-soybean rotation without cover crops (84%). Conversely, in the 5 to 15 cm layer, no-till cropping systems scored lower for overall soil function (58% to 61%) than mulch-till systems (65% to 66%). In the 0 to 5 cm layer, biological soil quality under the diversified no-till system with cover crops was 11% greater than under no-till without cover crops, and 20% greater than under mulch-till without cover crops. The effect of rotation phase was primarily reflected in 64% lower mineralizable N following corn relative to soybean. Additionally, soil nutrient function was significantly affected by biomass removal. The results of this study demonstrate that the benefits of conservation management practices extend beyond soil erosion reduction and improved water quality by highlighting the potential for enhanced soil quality, especially biological soil function. In particular, implementing conservation management practices on marginal and degraded soils in the claypan region can enhance long-term sustainability in annual cropping systems and working grasslands through improved soil quality.