Carbon reserve use is a major drought response in trees, enabling tree survival in conditions prohibiting photosynthesis. Still, regulation of starch metabolism under drought at the whole-tree scale is poorly understood. Our main questions were: (1) How do requirements of carbon storage and use are balanced at cell, tissue, and whole-tree scale? (2) What are the cellular components enabling fast carbon supply from starch degradation during a heat wave? (3) How is carbon allocation during recovery managed at the molecular level? To address these questions, we combined measurements of non-structural carbohydrates (NSC), tree physiology and starch metabolism enzymes expression. The experiment was conducted on twelve olive trees under seasonal warming and drying. Photosynthesis decreased in dried trees from 19 to 0. 5 µmol m-2 s-1 along the drought period. There was a fast heat-induced starch degradation, from 3.8% to 0.7%, which was reversed in a week in watered trees only. Mannitol production was a major drought response, constituting up to 71% and 41% out of total NSC in shoots and roots, respectively. We identified the gene family members relevant to long-term, whole-tree, carbon storage. Partitioning of function among beta-amylase and starch synthase family members were identified, with some members up regulated throughout drought while other members in recovery. Daily starch metabolism machinery was different from the stress-mode starch metabolism machinery when some genes are unique to the stress-mode response. Our results demonstrate specific, stress-related, starch metabolism genes, correlated with NSC fluctuations during drought and recovery.