Land use and land cover changes greatly influence surface characteristics and consequently the energy and mass exchange between the surface and the atmosphere. Recently, undisturbed lands and/or lands previously on conventional agriculture have seen land use changes towards biofuel crop production as part of climate change mitigation. To assess carbon balance of such lands, we converted three grasslands that were managed under the USDA Conservation Reserve Program (CRP) and three croplands that were in conventional agriculture (AGR) as corn/soybean rotations into annual (grain) and perennial (cellulosic) biofuel crops at the Kellogg Biological Station LTER sites in the US Midwest. One CRP grassland was also maintained to serve as a reference (Ref). We employed eddy covariance (EC) technique over all sites in order to examine the temporal long-term dynamics (2009-2014) of carbon NEE in response to land use conversion and management practices. The carbon balance of the field was achieved by accounting for the biomass or grain harvested from the field. We found that converting existing grasslands into annual or perennial crop production results into net carbon emission to the atmosphere that may take several years to balance. Carbon emission was also higher for the annual (corn) than for the perennial (switchgrass and mixed-prairie) crops.