Bambara groundnut is one of the under-utilized African legume crops, valued for its nutritional and health benefits, and for which ongoing studies will help to distinguish its many landraces and select the promising one for breeding programs. To describe the polar metabolome of the seed from 21 Bambara groundnut landraces, untargeted metabolomics approach using UPLC-qTOF-MS (Ultra performance liquid chromatography-Quadrupole time of flight mass spectrometry) was performed. Metabolites belonging to varied compound classes were detected and identified. The total phenolic, flavonoid and anthocyanin contents varied from 0.75 to 17.71 mg GAE.g, 0.01 to 2.51 mg QUE.g and 0.03 to 1.31 mg CYE.g, respectively. Unsupervised statistics highlighted differences in the metabolome of different landraces. Principal component analysis revealed that caffeic and catechin conjugates are the most decisive marker compounds discriminating the landraces. This study provides the most complete map of metabolites in Bambara groundnut seeds and demonstrates that UPLC-qTOF-MS coupled with chemometric is an excellent tool for differentiation between landraces. These findings highlight the potential of Bambara groundnuts as an economic source of natural antioxidants for human consumption and food industries, and therefore open horizons to the industrial use of Bambara groundnut flours in the development of functional food and feed products.