Soil health can differ across cropping systems because of variation in edaphic and management factors. We evaluated how biological indicators of soil health (soil organic matter [SOM], permanganate oxidizable carbon [POXC], mineralizable carbon [MinC], autoclaved-citrate-extractable [ACE] protein, and potentially mineralizable nitrogen [PMN]) compared across four common Wisconsin cropping systems: grazed cool-season pastures, forage-based rotations that included perennial legumes or grasses, annual rotations receiving manure, and annual rotations receiving synthetic fertilizers. Biological indicators of soil health were up to 195% greater in pastures than other cropping systems. MinC, POXC and PMN were 10%-90% greater in forage-based rotations than annual cropping systems, but only MinC and POXC were greater in annual systems with manure compared to those without manure by 35% and 7%, respectively. Perennial vegetation and livestock integration offer the greatest potential to increase biological indicators of soil health in agricultural lands.