The physiological disorders superficial scald, bitter pit, and lenticel blotch pit severely compromise the commercial value of ‘Granny Smith’ apples. A number of chemical treatments are available to alleviate these disorders but they are unacceptable in the expanding organic market. The objective of this research was to study the effectiveness of prestorage treatments—delayed cooling and elevated temperature under ultra-low oxygen (ULO) atmospheres—as organic-friendly strategies to control these disorders. ‘Granny Smith’ apples were exposed to four different treatments: 1) conditioning temperature treatments (CTemp): 10 days at 3 °C or 30 days at 3 °C or 10 days at 20 °C, in air; 2) the same conditioning temperature treatments combined with an ultra-low oxygen (ULO) conditioning treatment of 0.2–0.5 kPa O2 and <0.5 kPa CO2; 3) 1-methylcyclopropene (1-MCP) treatment as a commercial control; and 4) untreated control fruit. After the prestorage treatment, fruit were stored for 90 or 150 days at 0 °C, and then held poststorage for 8 days at 20 °C before quality analysis. A combination treatment of temperature conditioning and ULO for 30 days at 3 °C achieved the best control of superficial scald, bitter pit, and lenticel blotch pit. The use of ULO with CTemp for 10 days at 20 °C offered the same control but induced high concentrations of ethanol and acetaldehyde that affected the organoleptic acceptability of the fruit and reduced its commercial value. The use of 1-MCP offered 100% control of superficial scald but bitter pit and lenticel blotch pit disorder incidences were similar or higher than in the control fruit. All ULO conditioning treatments resulted in high ethanol and acetaldehyde concentrations during the first 90 days of storage, but fruit exposed to ULO conditioning treatment for 30 days at 3 °C showed similar organoleptic acceptability to control fruit after 150 days. Therefore, ULO conditioning is a potentially useful treatment for the organic apple industry.