Establishment of native grasses is a primary objective of restoration in Pinus ponderosa var. scopulorum (P. & C. Lawson) forests in the southwestern United States. Interactions among native grasses and soil microorganisms generate feedbacks that influence the achievement of this objective. We examined soil chemical properties and communities of plants and soil microorganisms in clear-cuts and P. ponderosa stands thinned and maintained at low and medium tree densities for over 40 years along with high density (unthinned) stands. Phospholipid fatty acids (PLFA) in soils were analyzed to examine arbuscular mycorrhizal (AM) fungi and microbial communities in the three thinning treatments and the unthinned stands with and without a recent broadcast burn. Additionally, two native bunchgrasses, Festuca arizonica and Muhlenbergia wrightii were grown in containers filled with intact soil cores collected from each field plot to more thoroughly compare the abundance of AM fungi and microbial communities across different stand densities and burn treatments. Tree thinning decreased litter cover and increased the abundance and diversity and altered community composition of both herbaceous vegetation and AM fungi. In the mineral soil layer, the pH, total carbon, nitrogen, phosphorus and PLFA profiles did not differ significantly among the four stand density or burn treatments. Mycorrhizal colonization of the container grown grasses did not significantly differ with tree density or burn treatments; however, F. arizonica roots had a strong trend for decreased colonization when grown in soil from high density (unthinned) tree cover. Soil from the containers with F. arizonica had a greater abundance of AM fungal spores. Furthermore, bacterial community composition varied with grass species. Concentration of biomarkers for bacteria were higher in soil that supported F. arizonica compared to soil in which M. wrightii was grown. Our results indicate that the creation of clear-cut openings in forests may increase the abundance and richness of AM fungal propagules and soil bacterial communities were surprisingly resilient to tree thinning and low-intensity fire treatments. These results suggest managing forests to create clear-cut openings generate conditions that favor understory native grasses and AM fungi that are linked to soil bacterial communities.