Sago starch (Metroxylon sagu) is derived from tropical palm tree which widely cultivated across Southeast Asia and Pacific islands. It serves as an important staple crop and is widely recognized for its nutritional and functional properties. However, the biochemical drivers of its characteristic flavor and market quality remain poorly understood. By harnessing the sensitivity and versatility of gas chromatography-mass spectrometry (GC-MS), this chapter introduces a standardized protocol for metabolomic profiling of sago flour. Starting from sample storage, through optimized solvent extraction and derivatization, to GC-MS acquisition and data processing, each step is designed to maximize sensitivity to both volatile and nonvolatile metabolites while ensuring reproducibility and comparability. By providing clear, validated protocols, we aim to enable robust characterization of the metabolites that shape sago starch’s taste and aroma, ultimately supporting quality control and product development in the sago industry.