Abstract Key message Quercus roburseedling mass was affected more by planting density than by taproot pruning. Root pruning enhanced stem biomass at the expense of roots in later growth stages. Alteration of biomass allocation due to nursery practices may result in greater susceptibility to injury and death of the seedlings under unfavorable environmental conditions. Context Plants adjust their growth and modulate the resource allocation in response to applied treatments and environmental conditions. Aims The aim was to examine how taproot pruning in seedlings grown at different densities affected long-term growth of Quercus robur. Methods Seedlings, sown as acorns at two planting densities, with or without pruned roots were harvested in the second, fourth, and fifth years of growth. The effect of root pruning on biomass allocation was determined by measuring leaf, stem, and root mass fractions; carbohydrate concentrations in the roots; and C/N ratios. Specific leaf area and root length were also determined to assess morphological adaptations to growth conditions. Results Total seedling mass was affected more by planting density than by taproot pruning. After 4 years of growth, root mass fractions were lower and stem mass fractions were greater in seedlings planted at a higher density. Five-year old root-pruned seedlings also had a lower root mass fraction and higher stem mass fractions than unpruned seedlings. Specific root length was not affected by root pruning or planting density. Conclusion Decrease of relative root biomass with simultaneous increase of stem biomass may be a long-term consequence of taproot pruning of Q. robur, and the effects may manifest years after the seedling stage.