In order to ensure a soil system’s sustained ability to carry out ecosystem services, indicators that assess soil health are needed. We examined the capacity of nematode maturity index (MI), structure index (SI), enrichment index (EI), and trophic groups as measures of soil health, by determining soil nematodes’ sensitivity to cropping systems: rotation, perturbation, fertilization, and inoculation with local effective microorganisms (LEM). Plots were managed for two years under different rotations, annual ryegrass/fallow (ARF) and cereal rye/edamame soybean (CRS). In the third year of the study, all of the plots were managed exactly the same as a wheat/edamame rotation. Data were collected in both winter and summer of this year. In all three years, three inoculant treatments (LEM, False-LEM and No inoculate) were applied. In CRS plots, which received the most tillage and fertilization, there were greater SI values in soils that received LEM application. Nematode community structure described by each MI, SI, and EI were sensitive enough to reflect changes due to differences in soil management practices from previous years. Principal components analysis confirmed that nitrogen mineralization is an important measure to include when using nematode community analysis in the development of a soil health index.