Willow (Salix spp.) short-rotation coppice (SRC) systems are productive bioenergy feedstocks that can be cultivated on marginal land and generate high yields when amended with nitrogen (N) fertilizers. However, fertilizer application results in greater N2O emissions and negates the potential carbon (C) neutrality of willow bioenergy systems. We evaluated 1) the effect of N fertilizer application on the soil-atmosphere exchange of CO2-C and (N2O-N emissions, soil NH4+-N and NO3--N); 2) emissions generated during winter and freeze-thaw cycles (FTCs); and 3) the net annual emission (CO2-equivalents [CO2-eq]) from willow SRC systems. CO2-C emissions followed seasonal trends with elevated emissions occurring in the spring and summer. Significantly greater (p < 0.05) CO2-C emissions were observed during the growing season, whereas only 7.2%-13.4% of the total CO2-C emissions occurred during the winter. Freeze-thaw cycles (FTCs) did not significantly (p < 0.05) increase CO2-C emissions. Nitrogen fertilizer application increased soil NH4+ and NO3- availability resulting in an N2O-N hot moment following fertilizer application in the spring. There was a N2O-N hot moment following FTC events, and winter N2O-N emissions were minimal. Overall, N2O-N emissions accounted for 2.2-3.4% of the total annual emissions. Willow SRC systems were a C sink in fertilized treatments with a C sequestration potential of 10.79 Mg CO2-eq ha(-1) yr(-1). Unfertilized treatments were a slight C source, with net emissions of 1.19 Mg CO2-eq ha(-1) yr(-1). We recommend a low rate of fertilizer application to willow SRC systems to maintain these systems as a long-term C sink.