Within the framework of energy biomass production, Arundo donax L. is very promising for its capability to grow on marginal lands with high yields. This potential can be realized in unused polluted areas where the energy production can be coupled with phytoremediation, and harvested biomass represents a resource and a means to remove contaminants from the soil. Two main processes are considered to evaluate A. donax L. biomass as an energy crop, determined by the timing of harvest: anaerobic digestion with fresh biomass before winter and combustion (e.g., pyrolysis and gasification) of dry canes in late winter. The aim of this work was to evaluate the use of A. donax L. in an area polluted by heavy metals for phytoextraction and energy production at two different harvest times (October and February). For that purpose, we established in polluted area in northern Italy (Caffaro area, Brescia) an experimental field of A. donax, and included switchgrass (Panicum virgatum L.) and mixed meadow species as controls. The results obtained by ICP-MS analysis performed on harvested biomasses highlighted a differential uptake of heavy metals depending on harvest time. In particular, considering the yield in the third year, A. donax was able to remove from the soil 3.87 kg ha−1 of Zn, 2.09 kg ha−1 of Cu and 0.007 kg ha−1 of Cd when harvested in October. Production of A. donax L. for anaerobic digestion or combustion in polluted areas represents a potential solution for both energy production and phytoextraction of heavy metals, in particular Cu, Zn and Cd.