Conventional agricultural cropping systems in the United States Midwest consist of short corn (Zea mays L.)-soybean (Glycine max L.) rotations that depend heavily on external inputs like chemical fertilizer and pesticides to maintain high yields. These simplified systems are associated with environmental externalities like soil degradation and water quality impairment. Agricultural systems that increase crop rotation diversity are known to increase yields compared to more simplified rotations, a phenomenon called the ‘rotation effect’. Mechanisms for this effect are not known, but could be linked to soil health changes. This study evaluates soil health in a conventional cropping system and an economically comparable alternative that previously demonstrated significantly greater corn and soybean yields than the conventional system. Using a long-term cropping system, 15 years after its establishment, soils in the corn phase were compared in the following cropping systems: 1) a conventional corn-soybean cropping system receiving mineral nitrogen fertilizer, and 2) a diversified corn-soybean-small grain+alfalfa (Medicago sativa L.)-alfalfa rotation receiving composted cattle manure and reduced mineral nitrogen fertilizer. A total of 37 soil health parameters were analyzed throughout the 2017 growing season, including 5 physical, 21 chemical, and 11 biological soil health parameters. Soils were sampled at depths of 0-15 cm and 15-30 cm, and some parameters were collected at three proximities to the corn root (interrow, row, and rhizosphere soil). Specific soil health parameters analyzed were: bulk density, soil hardness, water stable aggregates, plant available water, gravimetric water content, nine plant available nutrients (Al, Ca, Cu, Fe, K, P, Mg, Mn, and Zn), pH, cation exchange capacity, soil organic C (SOC), total soil N (TN), the ratio of SOC to TN, dissolved organic C, dissolved organic N (DON), dissolved inorganic N as soil nitrate and ammonium, total dissolved N (TDN), soil water nitrate, earthworm and mesofauna abundance, microbial biomass C, microbial biomass N, the ratio of microbial biomass C:N, soil CO2 respiration, and five hydrolytic enzyme activities (β-glucosidase, cellobiohydrolase, β-N-acetylglucosaminidase, acid phosphatase, and leucine aminopeptidase). Compared to the conventional system, the integrated livestock system increased physical soil health by 17.7%, chemical soil health by 22.6%, and biological soil health by 15.6%. Compared to the conventional system, implementation of crop rotation diversity and manuring reduced compaction and enhanced soil water content through the dry summer. The diversified system also increased nutrient storage and availability with greater CEC and pH. The alternative system enhanced the quantity and distribution of dissolved organic nutrients and microbial biomass, and increased earthworm populations, compared to the conventional system. Surprisingly, however, soil respiration was significantly greater in the conventional system compared to the diversified system, and may suggest physiological/metabolic differences in soil communities. The proportion of TDN as DON, in the diversified system was greater than in the conventional system, and effectively reduced the standing soil nitrate pool. Spring nitrate concentration in soil water under the diversified system was significantly less than the conventional system, and suggests reduced nitrate leaching potential when soil is most vulnerable to leaching. This analysis found that improvements in crop yield in the diversified system were not the result of a few increases in select soil health parameters, but likely a combined effect of multiple soil health improvements, relative to the conventional system. This diversified cropping system is an effective alternative to conventional cropping systems, for increasing soil health and reducing negative environmental impact, without compromising farm profitability.