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Gardiner Basin (GB) outside of Roosevelt Arch in Yellowstone National Park has been influenced not only by multiple geological events but also by the activities of human settlement for over 200 hundred years. With activities ranging from ranching and hay production to a rail line terminus with associated town, many negative effects on soil properties can be identified. These combined activities make restoring native vegetation to GB a complex task. The restoration effort began in 2008 with the construction of three large animal exclosures in which herbicides have been applied to eliminate invasive exotic plant species, primarily Alyssum desertorum and Agropyron cristatum, and cereal grains have been planted to stabilize the soil. In soils from inside and outside the exclosures we determined soil pH, extractable nitrogen (N), and organic matter (OM) to identify edaphic properties and quantified the abundance and diversity of soil microbes using molecular, microscopic, and physiological assays. The three sites vary predictably based on previous geologic activity with soil pH from 6.6 to 7.8, soil extractable N from 0.8 to 2.2 mg/kg soil and OM from 0.8 to 1.5%. The presence of invasive species significantly reduces the abundance and diversity of soil microbes while herbicide treatment had no detectable effects. OM, soil extractable N, and microbial diversity and abundance significantly increased over time with increasing cover crop plantings. Our data demonstrates that the management strategies employed to date in the GB restoration project are having beneficial effects on the soil microbial community and are reestablishing a functional soil community which will benefit the establishment of seeded native plant species.