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The objective of this study was to determine the effects of long-term annual beef manure amendments and wheat and rye cover crops on selected chemical, physical and biological properties of a typical Midwest U.S. soil under corn silage production. The treatments included: manure application/cover crop, manure application/no cover crop, no manure/cover crop, and no manure/no cover crop each sampled at three depths (0 to 7.5, 7.5 to 15, and 15 to 30 cm). Using beef manure significantly increased the total, organic, and microbial biomass carbon by over 60%, 40%, and 125%, respectively, when compared with commercial fertilizer. Planting a cover crop also significantly increased soil concentrations of total, organic, and biomass carbon; however the level of increase was not as dramatic as the fertilizer treatment. Using beef manure as a fertilizer significantly increased total, organic, and microbial biomass nitrogen and nitrate-nitrogen in the upper 30 cm profile by 78%, 75%, 130% and 130%, respectively. Annual applications of beef manure applied to meet the entire nitrogen needs of a corn silage crop resulted in excessively high Bray-phosphorus concentrations for the surface horizons particularly for the 0-7.5 cm depth. High water soluble P (WSP) concentrations were measured in the upper 0-15 cm depth of the treatment receiving annual beef manure applications. Use of a cover crop on the beef manure treatments increased the surface concentration of plant nutrients such as Bray-phosphorus and WSP. This indicates the importance of a cover crop for retaining mobile plant nutrients near the surface.