Reduction in energy sector greenhouse gas GHG emissions is a key aim of European Commission plans to expand cultivation of bioenergy crops. Since agriculture makes up 10–12% of anthropogenic GHG emissions, impacts of land-use change must be considered, which requires detailed understanding of specific changes to agroecosystems. The greenhouse gas (GHG) balance of perennials may differ significantly from the previous ecosystem. Net change in GHG emissions with land-use change for bioenergy may exceed avoided fossil fuel emissions, meaning that actual GHG mitigation benefits are variable. Carbon (C) and nitrogen (N) cycling are complex interlinked systems, and a change in land management may affect both differently at different sites, depending on other variables. Change in evapotranspiration with land-use change may also have significant environmental or water resource impacts at some locations. This article derives a multi-criteria based decision analysis approach to objectively identify the most appropriate assessment method of the environmental impacts of land-use change for perennial energy crops. Based on a literature review and conceptual model in support of this approach, the potential impacts of land-use change for perennial energy crops on GHG emissions and evapotranspiration were identified, as well as likely controlling variables. These findings were used to structure the decision problem and to outline model requirements. A process-based model representing the complete agroecosystem was identified as the best predictive tool, where adequate data are available. Nineteen models were assessed according to suitability criteria, to identify current model capability, based on the conceptual model, and explicit representation of processes at appropriate resolution. FASSET, ECOSSE, ANIMO, DNDC, DayCent, Expert-N, Ecosys, WNMM and CERES-NOE were identified as appropriate models, with factors such as crop, location and data availability dictating the final decision for a given project. A database to inform such decisions is included.