These datasets are extracted from a study that explored metabolic signatures in adipose tissue from 181 adults from the Spanish GraMo cohort. Participants with mean age of 49 years (Interquartile range 35-60 years) and 53% of women, were selected among patients undergoing routine surgeries unrelated to an oncological process to obtain an adipose tissue sample. Adipose tissue was analysed using targeted and non-targeted metabolomics and lipidomics approaches. Targeted analysis was performed by LC-MS/MS using the AbsoluteIDQ p180 Kit (Biocrates Life Sciences AG, Innsbruck, Austria). The plates were analyzed on a QTRAP 6500+ mass spectrometer (Sciex) equipped with a Turbo IonDrive™ V source operating in positive electrospray ionization (ESI), and hyphenated to an Exion™ AD chromatographic system (Sciex). Non-targeted analysis was performed by liquid chromatography coupled to high resolution mass-spectrometry on a Q-Exactive Orbitrap™ mass spectrometer (Thermo Scientific) equipped with an electrospray ionization source and hybridized with an Ultimate 3000 chromatographic system (Thermo Scientific). The molecule separation was performed in reversed-phase liquid chromatography with an Acquity ultra performance liquid chromatography charged surface hybrid C18 chromatographic column (100 mm × 2.1mm, 1.7 µm, Waters, USA). The raw data of positive and negative modes were then converted into open access format (mzML) with MSConvert software (Proteowizard). The Peakpicking workflow operates with XCMS R package. Data-dependent acquisition files were processed with msPurity workflow in Galaxy workflow4metabolomics. The outputs obtained were then uploaded to MassBank and MoNA to match with spectral libraries, and to SIRIUS to get in silico annotation. Confidence on the annotation process was documented according to the Schymanski scale.