Metabolomics, a comprehensive analysis of metabolites in biological sample, has been exhaustively used in food science and nutrition research, including research about legumes. Legumes such as soybean, edamame, and other beans have medicinal benefits that are reflected in their metabolites, such as essential amino acids, fibers, and isoflavones. Not only in the legumes themselves, but the product derivatives also show to have numerous medicinal benefits, such as tempe, that are able to replace meat as a protein source. One of the instruments that has been extensively used for metabolomics of legumes is gas chromatography/mass spectrometer (GC/MS). Two treatments that are able to help legume samples to be detected in GC/MS are extraction and derivatization. The extraction that will be discussed here is based on the Bligh-Dyer method, while the derivatizations are oximation and silylation. Several research have been conducted for analyzing legume-based products using a GC/MS instrument, such as bean analysis, fermentation process in legumes, and different metabolite profiles of legumes. The detailed methodology for analyzing legumes and legume-based products is depicted in this book chapter to let the readers understand the methodology that needs to be conducted to ensure high-quality data for legume GC-MS analysis.