The soil microbial community plays a crucial role in maintaining ecosystem health and sustainable integrity. The objective of this study was to determine the progress of ecosystem recovery in soils under a federal conservation reserve program (CRP) by examining several microbial community-related soil health indicators. Three adjacent soil ecosystems were evaluated, including conventional crop production, undisturbed (>30 years) land, and marginal land that was formally cultivated and has been under CRP for six years. The latter two ecosystems contained similar mixed perennial vegetation, whereas the former was cultivated with winter wheat, Triticum aestivum L. Soils were taken from these three ecosystems at two different locations twice a year for two consecutive years. Five replicate samples were taken from each ecosystem at each location during each sampling event. Soils were evaluated for water-stable aggregation and composition and structure of the soil microbial community using fatty acid methyl ester analysis. Roots isolated from soils were evaluated for arbuscular mycorrhizal intra-radical colonization. Preliminary results indicate that after six years of conservation, the soil ecosystems under CRP are not significantly different from their actively farmed counterparts. A typical contract with the CRP lasts 10-15 years. If the purpose of the program is to return the marginal land to its pre-cultivated conditions, more time may be required than what is currently allotted.