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Corky disorders in apples represent a significant problem for long-term storage where controlled atmosphere (CA) is mainly used. Ultra-low oxygen (ULO) is an alternative to CA, which consists of low partial pressure of O2 to maintain a low metabolism in the apple fruit, achieving an effective decrease in the ethylene production and physiological disorders. The aim of this research was to study the effectiveness of a short hypoxia period on the development of cork physiological disorders during the storage of apple. ‘Fuji’ apples were prestored under ULO (0.5 kPa O2) for two periods of time (15 and 30 days) and at two temperatures (0 or 5°C). Corky physiological disorders increased at 5°C prestorage temperature; however, ULO treatments for 15 or 30 days at 0 or 5°C achieved a significant reduction in corky disorders near to 1%, compared with control treatments. In addition, a considerable reduction in ethylene production for up to 30 days was observed in ULO-treated fruit at 0 and 5°C. ULO for 30 days at 0 and 5°C increased the internal production of ethanol and acetaldehyde, causing a lower sensory quality due to the presence of fermentative flavors in fruit stored at 5°C. ULO of 15 days of conditioning decreased the relative expression of ethylene biosynthesis genes MdACS1 and MdACO1, resulting in lower ethylene production.