Pesticide metabolites database is the overview of potential pesticide metabolites originated from selected parent compounds. These metabolites can be found in various source including JMPR (FAO/WHO) documents, EU pesticide database, EFSA etc. Based on their elemental formula respective ions (protonated / deprotonated molecules, their adducts) originated in ESI source can be derived for ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS). Occurrence data were obtained from determination of pesticide residues and their metabolites in samples of grapevine and wine, using UHPLC-HRMS, with the objective of supporting the possibility of the verification of the method of farming. It documents the identification of pesticide metabolites commonly used in conventional farming and provides a characterization of pesticide degradation during grapevine growth, maturation and during the wine-making process. The dataset is useful for anyone working on authentication of organic fruits and vegetables.