Mediterranean oaks commonly develop a strong main root reaching deep soil horizons before cotyledons emerge. In this way, seedlings may access deep soil water before the onset of drought. Root pruning –i.e. artificially altering apical meristems to induce secondary root development, may hamper this strategy, and it has been identified as a major factor causing seedling mortality. Nursery techniques to avoid or delay root pruning, such as the use of long containers, and reductions in the duration of the nursery phase, have been recommended. But scarce information is available on the functional role of the main root, and how it is altered by pruning. We evaluated the effect of clipping the main root’s apical meristem on the morphology, hydraulic conductivity and carbon fluxes of Quercus suber L. (Cork oak) seedlings. Unaltered main roots reached the bottom of 50-cm containers without branching 12 weeks after germination. Clipping apical meristems when the main root was 16.5 cm deep resulted in the development of 3-5 secondary roots ca. 1 mm thick close to the excised apex. Root length was higher and root average diameter lower in clipped than in unaltered seedlings. Clipped seedlings showed a marginally significant increase in root biomass and root weight ratio. Specific hydraulic conductivity of complete rooting system (high-pressure flowmeter), showed no significant effect of clipping. Instantaneous carbon fluxes were not affected by clipping. Our results suggest that root function may not be substantially altered by clipping, and secondary roots may take the functional role of a damaged main root.