Climate projections predict higher precipitation variability with more frequent dry extremes(1). CO2 assimilation of forests decreases during drought, either by stomatal closure(2) or by direct environmental control of sink tissue activities(3). Ultimately, drought effects on forests depend on the ability of forests to recover, but the mechanisms controlling ecosystem resilience are uncertain(4). Here, we have investigated the effects of drought and drought release on the carbon balances in beech trees by combining CO2 flux measurements, metabolomics and (13)CO2 pulse labelling. During drought, net photosynthesis (AN), soil respiration (RS) and the allocation of recent assimilates below ground were reduced. Carbohydrates accumulated in metabolically resting roots but not in leaves, indicating sink control of the tree carbon balance. After drought release, RS recovered faster than AN and CO2 fluxes exceeded those in continuously watered trees for months. This stimulation was related to greater assimilate allocation to and metabolization in the rhizosphere. These findings show that trees prioritize the investment of assimilates below ground, probably to regain root functions after drought. We propose that root restoration plays a key role in ecosystem resilience to drought, in that the increased sink activity controls the recovery of carbon balances.