The societal need for renewable energy from the agricultural sector offers new opportunities and challenges as we redefine ecosystem goods and services in view of sustainable land use and management under changing climates. There is a great potential for using crop residues as a feedstock for biofuel production in the United States, but developing this source should not decrease soil fertility or increase nutrient load. For example, harvesting excessive amounts of crop residue could have long-term impacts on soil quality, soil carbon stocks, and nutrient balances. The challenge is to develop cropping systems that can balance the demand for increased biofuel feedstock production with the maintenance of other critical ecosystem services. We use an innovative and integrated approach to quantify the impacts of increasing crop residue collection on the sustainability of agriculture and environmental quality.