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The role of carbon (C) and nutrient uptake, allocation, storage and especially their interactions in survival and recovery of trees under increased frequencies and intensities of drought events is not well understood. A full factorial experiment with four soil water content regimes ranging from extreme drought to well-watered conditions and two fertilization levels was carried out. We aimed to investigate whether nutrient addition mitigates drought effects on downy oak (Quercus pubescens Willd.) and whether storage pools of non-structural carbohydrates (NSC) are modified to enhance survival after 2.5 years of drought and recovery after drought relief. Physiological traits, such as photosynthesis, predawn leaf water potential as well as tissue biomass together with pools and dynamics of NSC and nutrients at the whole-tree level were investigated. Our results showed that fertilization played a minor role in saplings’ physiological processes to cope with drought and drought relief, but reduced sapling mortality during extreme drought. Irrespective of nutrient supply, Q. pubescens showed increased soluble sugar concentration in all tissues with increasing drought intensity, mostly because of starch degradation. After 28 days of drought relief, tissue sugar concentrations decreased, reaching comparable values to those of well-watered plants. Only during the recovery process from extreme drought, root NSC concentration strongly declined, leading to an almost complete NSC depletion after 28 days of rewetting, simultaneously with new leaves flushing. These findings suggest that extreme drought can lead to root carbon exhaustion. After drought relief, the repair and regrowth of organs can even exacerbate the root carbon depletion. We concluded that under future climate conditions with repeated drought events, the insufficient and lagged carbon replenishment in roots might eventually lead to carbon starvation and further mortality.