A field study was initiated in 1992 to investigate the long-term impacts of beef feedlot manure application (composted and uncomposted) on nutrient accumulation and movement in soil, corn silage yield, and nutrient uptake. Two application strategies were compared: providing the annual crop nitrogen (N) requirement (N-based rate) or crop phosphorus (P) removal (P-based rate), as well as a comparison to inorganic fertilizer. Additionally, effects of a winter cover crop were evaluated. Irrigated corn (Zea mays L.) was produced annually from 1993 through 2002. Average silage yield and crop nutrient removal were highest with N-based manure treatments, intermediate with P-based manure treatments, and least with inorganic N fertilizer. Use of a winter cover crop resulted in silage yield reductions in four of ten years, most likely due to soil moisture depletion in the spring by the cover crop. However, the cover crop did significantly reduce NO3-N accumulation in the shallow vadose zone, particularly in latter years of the study. The composted manure N-based treatment resulted in significantly greater soil profile NO3-N concentration and higher soil P concentration near the soil surface. The accounting procedure used to calculate N-based treatment application rates resulted in acceptable soil profile NO3-N concentrations over the short term. While repeated annual manure application to supply the total crop N requirement may be acceptable for this soil for several years, sustained application over many years carries the risk of unacceptable soil P concentrations.