The area used for bioenergy feedstock production is increasing because substitution of fossil fuels by bioenergy is promoted as an option to reduce greenhouse gas (GHG) emissions. However, agriculture itself contributes to rising atmospheric nitrous oxide (N2O) and methane (CH4) concentrations. In this study we tested whether the net exchanges of N2O and CH4 between soil and atmosphere differ between annual fertilized and perennial unfertilized bioenergy crops. We measured N2O and CH4 soil fluxes from poplar short rotation coppice (SRC), perennial grass-clover and annual bioenergy crops (silage maize, oilseed rape, winter wheat) in two central German regions for two years. In the second year after establishment, the N2O emissions were significantly lower in SRC (<0.1 kg N2O-N ha(-1) yr(-1)) than grassland (0.8 kg N2O-N ha(-1) yr(-1)) and the annual crop (winter wheat; 1.5 kg N2O-N ha(-1) yr(-1)) at one regional site (Reiffenhausen). However, a different trend was observed in the first year when contents of mineral nitrogen were still higher in SRC due to former cropland use. At the other regional site (Gierstadt), N2O emissions were generally low (<0.5.kg N2O-N ha(-1) yr(-1)) and no crop-type effects were detected. Net uptake of atmospheric CH4 varied between 0.4 and 1.2 kg CH4-C ha(-1) yr(-1) with no consistent crop-type effect. The N2O emissions related to gross energy in the harvested biomass ranged from 0.07 to 6.22 kg CO2 equ GJ(-1). In both regions, Gierstadt (low N2O emissions) and more distinct Reiffenhausen (medium N2O emissions), this energy yield-related N2O emission was the lowest for SRC. (C) 2015 Elsevier Ltd. All rights reserved.