Bioenergy crops have a secondary benefit if they increase soil organic C (SOC) stocks through capture and allocation belowground. The effects of four genotypes of short-rotation coppice willow (Salix spp., 'Terra Nova' and 'Tora') and Miscanthus (M. × giganteus ('Giganteus') and M. sinensis ('Sinensis')) on roots, SOC and total nitrogen (TN) were quantified to test whether below-ground biomass controls SOC and TN dynamics. Soil cores were collected under ('plant') and between plants ('gap') in a field experiment on a temperate agricultural silty clay loam after 4 and 6 years' management. Root density was greater under Miscanthus for plant (up to 15.5 kg m −3 ) compared with gap (up to 2.7 kg m −3 ), whereas willow had lower densities (up to 3.7 kg m −3 ). Over 2 years, SOC increased below 0.2 m depth from 7.1 to 8.5 kg m −3 and was greatest under Sinensis at 0-0.1 m depth (24.8 kg m −3 ). Miscanthus-derived SOC, based on stable isotope analysis, was greater under plant (11.6 kg m −3 ) than gap (3.1 kg m −3 ) for Sinensis. Estimated SOC stock change rates over the 2-year period to 1-m depth were 6.4 for Terra Nova, 7.4 for Tora, 3.1 for Giganteus and 8.8 Mg ha −1 year −1 for Sinensis. Rates of change of TN were much less. That SOC matched root mass down the profile, particularly under Miscanthus, indicated that perennial root systems are an important contributor. Willow and Miscanthus offer both biomass production and C sequestration when planted in arable soil.