Melons are prized for their characteristic aroma, however, pre-harvest growth, stage of ripening at harvest, post-harvest processing and storage conditions lead to quality changes in fresh-cut fruit. We considered changes in metabolites and gene expression over 14 days storage to assess underlying mechanisms and identify potential quality markers. Overall, 99 volatile organic compounds (VOCs) were detected and VOC profiles discriminated between two melon seasons, cut-size, storage temperatures and storage time, although season affected their discriminatory power. Abundance of two VOCs fell rapidly and was not associated with cut size, indicating their use as markers for early changes post-processing. Non-acetate to acetate ester ratio differed between the seasons and correlated with changes in alcohol acyl-transferase (CmAAT1) gene expression. Furthermore, CmAAT1 expression clustered with two ester VOCs that may be potential new products of this enzyme. Season also strongly affected post-harvest sugar content, most likely attributable to meteorological differences during growth. Storage temperature and cut size affected expression of transcription factors ERF71, ERF106, and TINY, whose expression generally rose during storage, probably related to increased stress. Thus, although time × temperature of storage are key factors, pre-harvest conditions and fruit processing impact significantly gene expression and aroma loss post-harvest.