During the spring of 2006, three willow varieties (SV1, SX67 and 9882-41) were established on marginal land in an agroforestry tree-intercropping arrangement where plots of short rotation willows were planted between rows (spaced 15 m apart) of 21-year-old mixed tree species. As a control, the same varieties were established on an adjacent piece of land without established trees (conventional willow system). This study investigated the magnitude of carbon pools, fine root and leaf biomass inputs and clone yields in both the tree-based intercropping (agroforestry) and conventional monocropping systems. Willow biomass yield was significantly higher in the agroforestry field (4.86 odt ha-1 y-1) compared to the conventional field (3.02 odt ha-1 y-1). In both fields, varieties SV1 and SX67 produced higher yields than the variety 9882-41. Willow fine root biomass in the top 20 cm of soil was significantly higher in the intercropping system (3,062 kg ha-1) than in the conventional system (2,536 kg ha-1). Differences in fine root biomass between clones were similar to that observed for differences in biomass yield: SV1 > SX67 > 9882-41. Leaf input was higher in the intercropping system (1,961 kg ha-1) than in the conventional system (1,673 kg ha-1). Clonal differences in leaf inputs followed the same trends as those for root biomass and yield: SV1 > SX67 > 9882-41. Soil organic carbon was significantly higher in the agroforestry field (1.94 %) than in the conventional field (1.82 %). A significant difference in soil organic carbon was found between the three clones: soils under clone 9882-41 had the lowest soil organic carbon at 1.80 %.