The practice of harvesting forest residues is rapidly increasing due to rising demand for renewable energy. However, major concerns have been raised about the sustainability of this practice and its net impact on productivity, in particular through negative effects on the growth of subsequent tree crops. We measured height, diameter at breast height (DBH) and tree spacing density on 23-year-old second rotation stands of Sitka spruce (Picea sitchensis), following whole tree harvesting (WTH-of all above ground biomass, by cable crane) or conventional stem-only harvesting (CH) of the first rotation crop. Overall, WTH reduced tree DBH by 10.3% (p = 0.017), with weaker evidence that it may have reduced height (by 8.2%, p = 0.164) and stand basal area (by 15.3%, p = 0.101). However, treatment effects differed greatly between individual blocks and, analysed separately by block, significant differences (WTH plot trees smaller than CH plot trees) were most notable in the two more exposed south-facing blocks (where, in both cases, p < 0.01 for height and p < 0.05 for basal area). Variation in productivity between the experimental plots cannot simply be attributed to preharvesting site environment - no correlation was found between first rotation and second rotation productivity - nor was treatment effect explained by differences in tree spacing density. Treatment effects can be attributed to the removal of three to four times larger quantities of N, P and K in the tree biomass by WTH than by CH of the first rotation crop, combined with greater competition with tree natural regeneration and other vegetation in WTH plots during the early stages of the second rotation. Soil moisture was higher in WTH plots but there was no evidence that WTH increased soil acidity or aluminium mobility nor that it decreased soil organic matter. The results also highlight the complexities of predicting the effect of harvesting treatment on future productivity, even within single-age, single-species forests. The study demonstrates the risk that WTH can reduce second rotation productivity of conifer forests in acidic upland sites, and that this practice will only be sustainable with appropriate interventions to overcome shortage of nutrients and high levels of vegetation competition.