Agricultural residues (prunings) coming from permanent plantations and orchards constitute a significant and largely unused potential for renewable energy. The EuroPruning project, respecting the impact on the environment, aims to turn prunings into a valuable fuel source by developing solutions for their harvesting, transportation and storage that will create growth in the European biofuels market. To determine the environmental consequences of the Pruning-to-Energy (PtE) logistics chain, a Life Cycle Assessment study will be conducted. In this study the PtE scenarios will be compared to three current practices: open field burning, mulching and use for domestic heating. In the paper an outline of the assessment methodology and consequent challenges are provided.