The quality of the cacao bean is determined by its biochemical compounds, including both related to nonvolatile and volatile components. This makes the study of metabolomic profiles in cacao an essential approach to identifying key metabolites associated with high-quality cocoa products. Metabolomics is a powerful and robust method for uncovering biochemical compounds present in cacao bean samples. However, the metabolites detected can vary significantly depending on the analytical method used. This chapter provides a comprehensive overview of metabolomic analysis for cacao beans, focusing on both volatile and nonvolatile compounds. Gas chromatography-mass spectrometry (GC-MS) is highlighted as a versatile analytical tool that can be applied to both volatile compounds and nonvolatile compounds through derivatization. The chapter outlines essential procedures, including sample preparation, extraction techniques, and analytical conditions, while emphasizing critical factors for optimizing the analysis to ensure reliable and meaningful results.