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Objectives The aim of this study is to determine the mechanism through which 1-methylcyclopropene (1-MCP) affects the quality of red 'Fuji' apples, which were stored for a short duration. Materials and Methods Red 'Fuji' apples were treated with 1-MCP (1.0 μl/L), stored at 25 °C for 0, 12, 24, 48, 72, and 96 h, and ethylene production was measured. An integrated metabolomic and transcriptomic analysis was performed on apples stored for 24 h. Results The release of ethylene was significantly delayed from red 'Fuji' apples subjected to 1-MCP treatment. By performing an integrated transcriptome and metabolome analyses, we identified 117 differentially expressed genes (DEGs) and 44 differentially accumulated metabolites (DAMs). By performing functional enrichment analysis, we found that DEGs were involved in the following pathways: carbon metabolism (LPD2 , gpmA , LTA2 , ACC , PSAT1 , MdCAS2), phytohormone signal transduction (EBF1), amino acid metabolism (MdACS-1), fatty acid metabolism (LOX1.5 , KCS4 , KAS1), energy metabolism (Lhcb1 , Lhcb6 , PsbY , GPDHC1 , PUMP5), metabolic pathways (TRE1 , HEXO1) and cell wall metabolism (CSLG2). Thus, these DEGs were involved in the ripening of fruits, and they controlled the quality of fruits at the post-harvest stage. The metabolites were enriched with DAMs. These were found to be individually involved in the metabolic pathway, secondary metabolite biosynthesis, phenylpropanoid biosynthesis, flavonoids, and flavonol synthesis. Conclusions The results indicate that 1-MCP inhibits the biosynthesis of ethylene and suppresses energy metabolism. Moreover, it also downregulates metabolic pathways and the enzymatic genes related to fruit quality. Therefore, 1-MCP delays the ripening of fruits at the post-harvest stage. This study helps us understand how 1-MCP treatment affects the ripening and quality of fruits. [ABSTRACT FROM AUTHOR]