Abstract The effect of rootstocks on flavor-related compounds, and nutrition and processing quality of Kinnow mandarin (C. nobilis × C. deliciosa) was investigated by targeted metabolomics approach employing LC–MS/MS and GC–MS/MS. Fruit samples were collected from mature trees grafted on six rootstocks, viz. Rough lemon 1 (C. jambhiri Lush), Rough lemon 2 (C. jambhiri), Sour orange (C. aurantium ‘Karun Jamir’), Cleopatra mandarin (C. reshni), Pectinifera (C. × depressa ‘Pectinifera’), and Shekwasha (C. × depressa ‘Shekwasha’). The data revealed significant differences in the concentration of some primary and secondary metabolites. Sour orange rootstock showed a higher concentration of polyphenolics and limonoid aglycones and a lower concentration of sugars, organic acids and aroma volatiles as compared to Shekwasha and Pectinifera. Rough lemon and Cleopatra rootstock presented desired concentration of organic acids and limonoid aglycones with moderate concentration of vitamins (B-complex and C), polyphenolics, and aroma volatiles. Principal component analysis (PCA) segregated Kinnow fruit grafted on different rootstocks into different PCs based on primary and secondary metabolites. Such differences indicate the influence of rootstock on Kinnow metabolome. This study highlights the importance of metabolomics in illuminating metabolic profile of citrus, thereby aiding in the selection of the desired rootstock for intended fruit quality.