Background: Brewer's spent grain (BSG) is one of the main by-products of beer industry, little used because of its high moisture making it difficult to transport and store. Mainly used as animal feed and for energy production, the agro-industrial waste have recently attracted attention as source of bioactive compounds, with potential applications in many sectors as food, nutraceutical, pharmaceutical, cosmetic, food packaging. The present work focuses on BSG as potential source of valuable small-size bioactive compounds. Methods: Laboratory-made BSG was obtained by using four base malts for mashing. After drying, BSG was eco-friendly extracted with water and the extracts analyzed by untargeted ElectroSpray Ionization (ESI)-Mass Spectrometry (MS)/Mass Spectrometry (MS) (ESI-MS/MS) infusion experiments and by targeted High Performance Liquid Chromatography-PhotoDiodeArray-ElectroSpray Ionization-Mass Spectrometry (HPLC-PDA-ESI-MS) in Selected Ion Recording (SIR) mode analysis, to investigate the metabolic profile, the phenolic profile, the individual phenolic content, and tryptophan content. Aqueous extracts of malts and wort samples were also analyzed for a comparison. Data were statistically analyzed by ANOVA test. An explorative analysis based on Principal Component Analysis (PCA) was also carried out on malts, wort and threshes, in order to study correlation among samples and between samples and variables. Results: The untargeted ESI-MS/MS infusion experiments provided the mass spectral fingerprint of BSG, evidencing amino acids (γ-aminobutyric acid, proline, valine, threonine, leucine/isoleucine, lysine, histidine, phenylalanine and arginine) and organic and inorganic acids (pyruvic, lactic, phosphoric, valerianic, malonic, 2-furoic, malic, citric and gluconic acids), besides sugars. γ-Aminobutyric acid and lactic acid resulted predominant among the others. The targeted HPLC-PDA-ESI-MS in SIR mode analysis provided the phenolic profile of the polar fraction of BSG, evidenced tryptophan as the main residual metabolite in BSG (62.33-75.35 µg/g dry BSG), and catechin (1.13-4.24 µg/g dry BSG) as the representative phenolic antioxidant of not pre-treated BSG samples. The chemometric analysis of the individual compounds content in BSG, malt and wort evidenced similarities and differences among the samples. Conclusions: As main goal, the phytochemical characterization of BSG from base malts highlighted BSG as a potential source of small biomolecules, as tryptophan and catechin, besides γ-aminobutyric acid and lactic acid, opening to new perspectives of application for BSG. Strategies for their recovery are a future challenge. Moreover, ESI-MS/MS analysis was confirmed as a powerful tool for fast characterization of complex matrix. Last, results obtained by chemometric elaboration of data demonstrated the possibility to monitor a small number of molecules to ensure the quality of a final product.