The drive to develop renewable energy is increasing the interest in energy forestry. Woody biomass from forest residues has the potential to make a significant contribution to greenhouse gas emission reduction through fossil fuel substitution. However, there is a danger of operational practice running ahead of the understanding of the environmental impacts of such activities. Consequently, there is an urgent requirement for scientifically underpinned guidance on the best management practices to ensure soil and water protection, including sustaining forestry’s key role in carbon capture. This study addresses the main issues associated with stump harvesting practices and their impacts on soil carbon and nutrient capital and effects on the second rotation tree growth. It reports results from a clearfell site in the UK where experimental stump harvesting was carried out in 2005 before replanting with Sitka spruce Picea sitchensis (Bon.)Carr. Both stump harvested and conventional harvested areas (Control) were studied in 2009 and 2010, five years after harvesting, on the two distinct soil types at the site: podzolised brown earth and peaty gley soils. Results show impacts of stump harvesting on soil carbon and nitrogen stocks, residual water, base cations (K+, Ca2+ and Mg2+) concentrations and stocks and bulk density in both soil types. The organic peaty gley soil showed larger and deeper profile changes after stump harvesting compared with the podzolised brown mineral soil, where some of the negative changes in C, N and base cations in the top soil were compensated by increases at depth. Tree assessment showed positive effect of stump harvesting on K and Ca uptake by young seedlings, but N and P nutrient status was reduced on the peaty gley soils. The overall results support the current UK forestry guidance for stump harvesting which identifies that soil type is the most important site factor determining the sustainability of the practice.