Technical Abstract: ‘Empire’ apple fruit are more susceptible to flesh browning at 3.3 oC if first treated with 1-methylcyclopropene (1-MCP), an inhibitor of ethylene perception. To better understand the metabolic changes associated with this browning, untargeted metabolic profiling with partial least squares analysis has been used to visualize changes in the metabolic profile during hypoxic controlled atmosphere (CA) storage, ethylene insensitivity, and disorder development. Overall, carbohydrates and organic acids were not appreciably affected by 1-MCP, the levels of amino acids and volatile metabolites were significantly influenced by 1-MCP treatment. Sorbitol and levels of some amino acids were elevated towards the end of storage in 1-MCP treated fruit. CA storage reduced the levels of many volatile components and 1-MCP reduced these levels further. '-Aminobutyric acid (GABA) was associated with the development of flesh browning symptoms. Unlike other volatile compounds, methanol levels gradually increased with storage duration, regardless of 1-MCP treatment, while 1-MCP decreased ethanol production. Results reveal metabolic changes during storage that may possibly associated with development of flesh browning symptoms.