Abstract:[Background] The pathogen responsible for quinoa Choanephora rot is Choanephora cucurbitarum. However, the metabolic changes of quinoa in response to the infection remain unclear. [Objective] We studied the changes of metabolites and key metabolic pathways in quinoa after infection with C. cucurbitarum, aiming to understand the physiological and biochemical mechanisms of the disease. [Methods] We employed non-targeted metabolomics and multivariate statistical analysis to investigate the changes in metabolites and metabolic pathways in quinoa stems after infection with C. cucurbitarum. [Results] Compared with the control, infection with C. cucurbitarum in quinoa resulted in 512 differential metabolites (P<0.01), including 283 upregulated metabolites and 229 downregulated metabolites. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed 19 main differential metabolites in the quinoa stems in response to infection (P<0.05). These differential metabolites were enriched in four metabolic pathways: arachidonic acid metabolism, linoleic acid metabolism, alpha-linolenic acid metabolism, and flavone and flavonol biosynthesis. [Conclusion] C. cucurbitarum infection leads to changes in arachidonic acid metabolism, linoleic acid metabolism, α-linolenic acid metabolism, and flavone and flavonol biosynthesis in quinoa. The accumulation of jasmonic acid from α-linolenic acid metabolism and the blocked biosynthesis of flavone and flavonol may be involved in the response of quinoa to C. cucurbitarum infection.