The Missouri Soil and Water Conservation Program was initiated by the Department of Natural Resources (DNR) to address challenges related to soil and water degradation by examining soil health under real-world management practices. Soil health data from 5,300 field sites enrolled in a DNR cost-share program were analyzed for the effects of tillage intensity [no-till (NT), reduced tillage (RT), and intensive tillage (IT)] and crop rotational diversity (monoculture, two-crops, and three or more crops in rotation) within and across six regions in the state. Soil health indicators included soil organic carbon (SOC), active carbon, potentially mineralizable nitrogen (PMN), and aggregate stability. At the state level, SOC, active carbon, and PMN were 14.4, 14.0, and 17.5% greater under NT, and 10.2, 11.0, and 11.2% greater under RT, respectively, compared with IT. Aggregate stability was greater under NT (33.8%) and RT (30.4%) relative to IT (28.0%). Across the state, diversified rotations with three or more crops exhibited 6.1 and 7.9% greater SOC, 6.5 and 7.9% greater active carbon, and 10.7 and 11.6% greater PMN relative to two-crop rotations or monocultures, respectively. Aggregate stability was significantly greater under diversified rotations (35.5%) relative to two-crop rotations (30.6%) and monoculture (30.8%). This study highlights the value of on-farm datasets from real crop production systems and illustrates the potential to increase soil health with adoption of conservation tillage and extended crop rotations in Missouri.