Flavour acceptance tests of ‘Wonderful’ pomegranate arils during prolonged storage under commercial modified atmospheres conditions yielded high preference scores during the first 12 weeks of cold storage at 7 °C, but sensory quality decreased remarkably after 16 and, especially, 20 weeks. Descriptive flavour analyses by a trained sensory panel revealed that the decrease in fruit flavour preference resulted mainly from a decrease in typical pomegranate flavour and increases in ‘overripe’ and ‘off-flavour’ odours. GC-MS analysis of aroma volatile contents revealed high correlations (r2 > 0.9) between accumulation of the ethanol fermentation products ethanol and ethyl acetate and the observed decrease in fruit flavour preference. In addition, we observed relatively high correlations (r2 > 0.7) between the accumulation of various sesquiterpene volatiles and the decrease in flavour preference. According to these findings, it is suggested that the decrease in flavour preference most likely resulted from massive accumulation of ethanol fermentation products and sesquiterpene volatiles.