The cultivation of energy cane throughout the Southeastern United States may displace grazed pastures on organic soil (Histosols) to meet growing demands for biofuels. We combined results from a field experiment with a biogeochemical model to improve our understanding of how the conversion of pasture to energy cane during early crop establishment affected soil GHG (CO2, CH4, and N2O) exchange with the atmosphere. GHG fluxes were measured under both land uses during wet, hot and cool, dry times of year, and following a fertilization event. We also simulated the impact of changes in precipitation on GHG exchange. Higher fertilization of cane contributed to greater emission of N2O than pasture during warmer and wetter times of the year. The model predicted that energy cane emitted more nitrogen than pasture during simulated wetter than drier years. The modeled emission factor for N2O was 20 to 30-fold higher than the default value from IPCC (1%), suggesting that the default IPCC value could dramatically underestimate the consequences of this land conversion on the climate system. Predicted soil CH4 and CO2 fluxes were higher in pasture than energy cane, and this difference was not affected by increasing precipitation. Model simulations predicted that soils under first year cane emit more GHGs than pasture, particularly during wet years, but this difference disappeared two years after energy cane establishment. Our results suggest that management practices may be important in determining soil GHG emissions from energy cane on organic soils particularly during the first year of cane establishment.