During postharvest storage at low temperatures, specific apple cultivars can develop a physiological disorder known as superficial scald. This disorder results with the formation of brown or black patches on fruit skin, compromising the entire fruit marketability. In this work, we investigated the effects of different storage strategies distinguished by a different regime of oxygen during the storage of two apple cultivars (‘Granny Smith’ and ‘Ladina’), both susceptible to superficial scald, but with a different magnitude. More precisely, the apples collected from the two cultivars were stored in regular and controlled atmosphere, for five and seven months, respectively. The controlled atmosphere was moreover carried out according to dynamic controlled atmosphere by means of chlorophyll fluorescence and ultra-low oxygen level strategy. After cold storage, apples were kept for one week in regular atmosphere at room temperature, to simulate shelf-life conditions. The apple skin was further collected, and the total amount of RNA was extracted to assess the global transcriptome. In the cultivar ‘Granny Smith’ it was observed that the storage approach carried out with low level of oxygen was efficient in preventing the development of scald symptoms, underlying the central role of the oxidative process in this mechanism. The RNA-Seq analysis highlighted that the samples subjected to the controlled atmosphere were characterized by a high expression of genes related to carbohydrate metabolism and lipid accumulation. ‘Ladina', instead, showed a different behaviour as low oxygen or 1- MCP was less effective in controlling the development of scald compared to ‘Granny Smith’. The different physiological response was also distinguished by a different transcriptional signature, with DEGs more related to ATP biosynthesis, ethylene production, and oxidative stress response. Comparative transcriptomics carried out between these two cultivars provides insights into the gene regulatory network involved in the development of superficial scald in apples.