Alternative manure application rates represent an integral part of current nutrient management efforts on animal feeding operations (AFOs). Previous studies have indicated that lower manure application rates tend to increase farm production costs. In this study, the Comprehensive Economic and Environmental Optimization Tool - Macro Modeling System (CEEOT-MMS) was used to evaluate the farm-level economic implications of alternative manure application rates for all AFOs in the 48 contiguous states of the U.S. Representative farms derived through statistical disaggregation of national databases and K-means clustering were simulated within the the Farm-level Economic Model (FEM) to determine the economic impacts of four manure application rates. The highest manure application rate scenario investigated here (two times the N rate, or 2N) resulted in the highest net farm returns to AFOs. Similarly, the lowest manure application rate scenario considered in this study (the Half P rate), is projected to cost AFO operators the most, about $4,300 relative to the standard N rate scenario. Results of the study show that the larger AFOs would be required to haul out a much greater portion of on-farm manure than the smallest AFOs. Furthermore, the largest AFOs incur the highest per farm and per animal unit costs when manure application rates are reduced to rates below the P rate. However, under the Half P scenario all farm size groups would be required to haul out significant portions of manure generated on the farm. The total annual cost of the Half P scenario tops $1 billion dollars for AFOs in the 48 contiguous states.