The exploitation of energy crops requires the assessment of their sustainability in terms of both economic and environmental cost. Among the agronomic practices applied for giant reed (Arundo donax L.) production, harvesting may weigh for a relative high percentage on the overall balance. Till now, conventional and modified machinery have been used for the production of different type of biomass (shredded, chipped, baled). In the present study an economic and energy analysis of harvesting systems and biomass transport has been conducted considering three actual cases of study representative of common harvesting systems in Italy and Spain: single-pass (chipping and loading) and two passes (mowing plus chipping and loading or crushing and windrowing plus baling). The aim of the work was to evaluate the cost-effectiveness and the environmental sustainability of the different options. The number of operations (single or two passes) did not weigh on the final result, and the economic criterion did not coincide with the energy one. The cost of harvesting for the single-pass system was the lowest (17.9€tdm−1), but the economic costs of the whole chain (harvesting and transport) were more convenient for baling, and the energy demand of both systems was similar. Evidence was provided that factors like type of machinery, effective field capacity, yield, moisture content, bulk density and crop uniformity influenced the harvesting costs (from both economic and energy viewpoints) and the delivery of the biomass from the field to the first collection point. Therefore, a case-by-case analysis is recommended in order to optimize the logistics of a particular bioenergy plant.