Soil microbial communities play an important role in agricultural soil ecosystems by regulating organic matter decomposition and plant nutrient availability. The temporal and spatial variation in soil microbial communities is influenced mainly by soil physical-chemical properties, themselves directly affected by management practices. The effect of tillage and nitrogen fertilization on soil physical-chemical properties and soil microbial communities was evaluated in a split block experiment with two primary tillage systems [moldboard plow (MP) and no-tillage (NT)] and two fertilizer nitrogen rates (0 and 168 kg N/ha). Treatment effects on physical properties (bulk density, texture, soil moisture), chemical properties (pH, total carbon and nitrogen, dissolved organic carbon and nitrogen, extractable ammonium and nitrate) and soil microbial community structure (PLFA profiles) were evaluated at two depths (0 to 5 cm and 5 to 15 cm) in spring 2004. Microbial biomass, total carbon and nitrogen, DOC, and soil moisture were highest, and bulk density lowest, for the 0 to 5 cm NT soils. The DON and soil clay were highest in the 5 to 15 cm NT soils. The 0 to 5 cm depth of the NT soils was enriched in eukaryotes and gram negative bacteria and depleted in actinobacteria and bacteria that reduced sulfate or iron. This latter group of organisms was also depleted in the 0 to 5 cm depth of soils amended at the greater fertilizer nitrogen rate. Soil pH was also lower in these soils, especially under no-tillage management. In short, soil physical-chemical properties, and consequently soil microbial community structure, were affected by tillage and nitrogen rate management.