Thua Nao, a traditional Thai fermented soybean product, is rich in diverse metabolites contributing to its unique flavor and nutritional profile. Gas chromatography-mass spectrometry (GC-MS) is a powerful analytical tool used to identify and quantify the volatile and semi-volatile compounds in fermented foods like Thua Nao. This chapter provides a detailed methodology for the extraction and derivatization of Thua Nao samples for GC-MS metabolomic analysis. The extraction involves lyophilization, methanol-based solvent extraction, centrifugation, and concentration under vacuum. Derivatization is performed through oximation with methoxyamine hydrochloride, followed by silylation using MSTFA. These steps ensure the effective detection of a broad spectrum of metabolites, including amino acids, organic acids, and volatiles. The protocol optimizes the conditions for sample preparation to improve the reliability and reproducibility of GC-MS analysis in fermented soybean products.