Decarbonization of the world's energy supply is essential to meet the targets of the 2016 Paris climate change agreement. One promising opportunity is the utilization of second generation, low input bioenergy crops such as Miscanthus and Short Rotation Coppice (SRC) willow. Research has previously been carried out on the greenhouse gas (GHG) balance of growing these feedstocks and land-use changes involved in converting conventional cropland to their production; however, there is almost no body of work understanding the costs associated with their end of life transitions back to conventional crops. It is likely that it is during crop interventions and land-use transitions that significant GHG fluxes might occur. Therefore, in this study, we investigated soil GHG fluxes over 82 weeks during transition from Miscanthus and SRC willow into perennial ryegrass in west Wales, UK. This study captured soil GHG fluxes at a weekly time step, alongside monthly changes in soil nitrogen and labile carbon and reports the results of regression modelling of suspected drivers. Methane fluxes were typically trivial; however, nitrous oxide (N2O) fluxes were notably affected, reverted plots produced significantly more N2O than retained controls and Miscanthus produced significantly higher fluxes overall than willow plots. N2O costs of reversion appeared to be contained within the first year of reversion when the Miscanthus plots produced an average pregrass flux of 0.13 mg N2O m−2 hr−1 while for willow, this was 0.03 mg N2O m−2 hr−1. Total N2O emission from reversion increased the carbon cost over the lifetime of the Miscanthus from 6.50 to 9.91 Mg CO2 eq. ha−1 while for the willow, this increase was from 9.61 to 10.42 Mg CO2 eq. ha−1. Despite these significant increases, the carbon cost of energy contained in these perennial crops remained far lower than the equivalent carbon cost of energy in coal. © 2018 The Authors. GCB Bioenergy Published by John Wiley & Sons Ltd.