Superficial scald is one of the most serious postharvest physiological disorders that may affect apples after a prolonged cold storage period. As little is known about its early determinism, we investigated the impact of pre- and post-harvest climatic variations on its incidence on a susceptible apple cultivar. Fruit batches with contrasted phenotype for superficial scald incidence were identified among several years of “Granny Smith” fruit production. The “low scald” year pre-harvest climate was characterised by a warm period followed by a sudden decrease in temperature, playing the part of an in vivo acclimation to cold storage. In agreement, a transcriptomic analysis at harvest revealed that many abiotic stress responsive genes were differentially expressed in fruit peel. In particular 48 Heat Shock Proteins (HSPs) and 5 Heat Shock transcription Factors (HSFs) were strongly induced at harvest when scald incidence was low after 4 months of cold storage. For “high scald” year, a post-harvest cold acclimation of 1 week was efficient to reduce scald incidence. Expression profiles of stress related genes were affected by the acclimation treatment and indicate fruit physiological adaptations to cold storage. The identified stress-responsive genes and in particular HSPs could be useful indicators of the fruit physiological status in order to predict the risk of scald occurrence as early as harvest.