Abstract Bioenergy crops are one of the renewable energy options available to decarbonise the energy sector in Scotland and help to achieve the overall planned target of 80% reduction in greenhouse gas (GHG) emissions by 2050. A process-based model for poplar and willow developed for simulating the effect of different environmental and management options on growth and biomass yield was used to estimate the GHG abatement potential (GHG-AP) under different crop management options in Scotland. The model results of annual wood yield did not show a strong relation with any of the environmental factors except that of initial soil organic carbon (SOC) content. Increasing plant density and decreasing harvest frequency increased GHG-AP. Application of N-fertilizers at a rate of 50–100 kg N ha−1 resulted in the buildup of carbon in soils with less than 180 Mg C ha−1. However, in soils with greater SOC contents, annual emissions resulting from N fertilizer application were greater than the carbon saving through marginal increases in wood yield and SOC changes. The best management scenario in terms of economic and environmental objectives depends on identifying an optimum plant density based on the site specific conditions with a fertilizer application of 20–100 kg ha−1 y−1 and a five year harvest interval. Even under the best economic scenarios, SRC willow and poplar have a GHG-AP ranging from 9.9 to 11.6 and 8.8–10.0 Mg CO2 eq. ha−1 y−1, respectively. Under the best environmental scenarios this range increases to 10.5- 13.2 and 9–11.1 Mg CO2 eq. ha−1 y−1 for willow and poplar, respectively.