Abstract:[Background] Sesame (Sesamum indicum L.) is an important oilseed crop susceptible to the infection by Alternaria alternata, which reduces the yield and subsequently impacts the security and quality of sesame. [Objective] This study investigated the differential metabolites and pathways in the sesame capsules infected by A.alternata, aiming to unveil the effects of this disease on sesame capsules. [Methods] Non-targeted metabolomics and multivariate statistical analysis were employed to analyze the metabolite differences and metabolic pathway changes in sesame capsules after infection by A. alternata. [Results] The metabolomic analysis revealed a total of 247 differential metabolites categorized into 11 classes in the capsule peel and seeds. Compared with the control group, A.alternata infection led to the up-regulation of 126 and 231 metabolites and down-regulation of 27 and 118 metabolites in the peel and seeds, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differential metabolites indicated that A.alternata infection significantly affected the amino acid, carbohydrate, and nucleotide metabolism in the peel and seeds, thereby impacting sesame quality. [Conclusion] A.alternata infection affects the quality of sesame by influencing amino acid and carbohydrate metabolism in the capsule peel and seeds. This study provides clues for revealing the disease mechanism and managing this pathogen, thereby contributing to agricultural sustainability.