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Untargeted metabolomics is a powerful tool with high resolution and the capability to characterize a wide range of bioactive natural products from fruit and vegetable by-products (FVB). Thus, this approach was applied in the study to evaluate the phenolic compounds (PC) by metabolomic screening in five FVB after optimizing their extraction. The total phenolic content and antioxidant activity analyses were able to select the best extractor (SM) and ultrasonication time (US) for each FVB; methanol was used as a control. Although ultrasonication yielded a lower number of PC identifications (84 PC), the US extract was the most efficient in total ionic abundance (+21% and +29% compared to the total PC and SM extracts, respectively). Ultrasonication also increased the phenolic acid (+38%) and flavonoid classes (+19%) extracted compared to SM, while the multivariate analyses showed the control as the most dissimilar sample. FVB extracted from the same parts of the vegetable/fruit showed similarities and papaya seed presented the most atypical profile. The application of the metabolomics approach increased the knowledge of the bioactive potential of the evaluated residues and possibilities of exploring and valorizing the generated extracts.