Second-generation bioenergy crops, including Short Rotation Forestry (SRF), have the potential to contribute to greenhouse gas (GHG) emissions savings through reduced soil GHG fluxes and greater soil C sequestration. If we are to predict the magnitude of any such GHG benefits a better understanding is needed of the effect of land use change (LUC) on the underlying factors which regulate GHG fluxes. Under controlled conditions we measured soil GHG flux potentials, and associated soil physico-chemical and microbial community characteristics for a range of LUC transitions from grassland land uses to SRF. These involved ten broadleaved and seven coniferous transitions. Differences in GHGs and microbial community composition assessed by phospholipid fatty acids (PLFA) profiles were detected between land uses, with distinctions between broadleaved and coniferous tree species. Compared to grassland controls, CO2 flux, total PLFAs and fungal PLFAs (on a mass of C basis), were lower under coniferous species but unaffected under broadleaved tree species. There were no significant differences in N2O and CH4 flux rates between grassland, broadleaved and coniferous land uses, though both CH4 and N2O tended to have greater uptake under broadleaved species in the upper soil layer. Effect sizes of CO2 flux across LUC transitions were positively related with effect sizes of soil pH, total PLFA and fungal PLFA. These relationships between fluxes and microbial community suggest that LUC to SRF may drive change in soil respiration by altering the composition of the soil microbial community. These findings support that LUC to SRF for bioenergy can contribute towards C savings and GHG mitigation.