This article evaluates the suitability of the ECOSSE model to estimate soil greenhouse gas (GHG) fluxes from short rotation coppice willow (SRC-Willow), short rotation forestry (SRF-Scots Pine) and Miscanthus after landuse change from conventional systems (grassland and arable). We simulate heterotrophic respiration (R h ), nitrous oxide (N 2 O) and methane (CH 4 ) fluxes at four paired sites in the UK and compare them to estimates of R h derived from the ecosystem respiration estimated from eddy covariance (EC) and R h estimated from chamber (IRGA) measurements, as well as direct measurements of N 2 O and CH 4 fluxes. Significant association between modelled and EC-derived R h was found under Miscanthus, with correlation coefficient (r) ranging between 0.54 and 0.70. Association between IRGA-derived R h and modelled outputs was statistically significant at the Aberystwyth site (r = 0.64), but not significant at the Lincolnshire site (r = 0.29). At all SRC-Willow sites, significant association was found between modelled and measurement-derived R h (0.44 ≤ r ≤ 0.77); significant error was found only for the EC-derived R h at the Lincolnshire site. Significant association and no significant error were also found for SRF-Scots Pine and perennial grass. For the arable fields, the modelled CO 2 correlated well just with the IRGA-derived R h at one site (r = 0.75). No bias in the model was found at any site, regardless of the measurement type used for the model evaluation. Across all land uses, fluxes of CH 4 and N 2 O were shown to represent a small proportion of the total GHG balance; these fluxes have been modelled adequately on a monthly time-step. This study provides confidence in using ECOSSE for predicting the impacts of future land use on GHG balance, at site level as well as at national level.