This study estimated the potential emissions of greenhouse gases (GHG) from bioenergy ecosystems with a biogeochemical model AgTEM, assuming maize (Zea mays L.), switchgrass (Panicum virgatum L.), and Miscanthus (Miscanthus × giganteus) will be grown on the current maize-producing areas in the conterminous United States. We found that the maize ecosystem acts as a mild net carbon source while cellulosic ecosystems (i.e., switchgrass and Miscanthus) act as mild sinks. Nitrogen fertilizer use is an important factor affecting biomass production and N2O emissions, especially in the maize ecosystem. To maintain high biomass productivity, the maize ecosystem emits much more GHG, including CO2 and N2O, than switchgrass and Miscanthus ecosystems, when high-rate nitrogen fertilizers are applied. For maize, the global warming potential (GWP) amounts to 1–2 Mg CO2eq ha−1 yr−1, with a dominant contribution of over 90% from N2O emissions. Cellulosic crops contribute to the GWP of less than 0.3 Mg CO2eq ha−1 yr−1. Among all three bioenergy crops, Miscanthus is the most biofuel productive and the least GHG intensive at a given cropland. Regional model simulations suggested that substituting Miscanthus for maize to produce biofuel could potentially save land and reduce GHG emissions.