This dataset contains LC-HRMS data from leaf hydro-methanolic extracts of twenty-four accessions of wild and cultivated tomato plants. The accessions included in this study were selected to represent a broad spectrum of genetic diversity (for more detail see Amegan et al., 2024, https://dx.doi.org/10.1127/entomologia/2024/2399). These comprised 6 Solanum lycopersicum accessions, in which both large-fruited varieties and cherry-type (var. cerasiforme) were considered together, as well as wild species such as Solanum cheesmaniae (10), Solanum habrochaites (6), and Solanum pennellii (2). All the accessions were provided by the CRB-Leg, INRAE Avignon. Seeds were pre-germinated in a controlled environment chamber at 24 ± 1°C, with 65 ± 5% humidity and a 16-hour light cycle. For S. cheesmaniae, seeds were previously soaked in bleach (2°4) for 30 min, to accelerate the degradation of the outer seed coat and, thereby, to promote germination. The germinated seedlings were grown in small cubic pots filled with a mixture of potting soil and perlite. Seedlings were placed in a climatic chamber under the following conditions : 24 ± 1 °C, 60–70% RH, 16:8h [light: dark] photoperiod. Two fresh leaflets from 4- to 6-week-old plants of each accession were harvested to prepare methanolic extracts according to Royer et al., 2013, https://doi.org/10.1016/j.phytochem.2012.12.003). LC-HRMS analyses were acquired on an Orbitrap IDXTM (ThermoFisher Scientific, Bremen, Germany) mass spectrometer in positive and negative electrospray ionization (ESI) modes. MS1 acquisition allowed the detection and quantification of 3764 features accross the 217 samples (24 accessions x 9-13 replicates). MS2 analysis was realized on a mixture of all samples which allows to obtain fragmentation data on 3412 features. Detection and quantification were realized using the software Compound Discoverer with an analytical workflow which parameters are described in the .txt file "Analytic_Workflow_Compound_Discoverer". The MS1 quantification on all samples is given as a spreadsheet (solanum data 14-11-25v2). The metadata connecting sample names to solanum accessions, species and subspecies is given as a spreadsheet (solanum metadata 14-11-25v2). MS2 data is contained in a .mgf file (HCD.mgf). Each MS file analysis has been generated as .raw (Thermo format). For accessibility considerations, each MS file has been converted in the generic format (.mzXML), with one file containing data acquired in positive mode (POS) and another file containing data acquired in negative mode (NEG). Those files are available in this repository. This dataset allows characterizing the intra- and inter-specific leaf metabolic diversity on cultivated and wil d tomato plants.