The chemical profile of young coconut (Cocos nucifera L.) is important in defining its physical, nutritional, and sensory qualities. Gas chromatography-mass spectrometry (GC-MS) is emerging as a powerful tool for investigating the chemical components of young coconuts. Since young coconuts contain high lipids and diverse metabolites, reliable analysis depends on thoughtful and consistent sample preparation. This chapter offers a comprehensive protocol for GC-MS-based metabolomic analysis of both liquid and solid endosperm of young coconuts, detailing key procedures such as sample preparation, extraction, and derivatization. It explains the rationale behind the method and provides practical guidance for performing GC-MS analytical workflows. Solving the challenges due to metabolite diversity and matrix composition, the protocol enables reliable compound identification even across various research studies. These methods can help researchers get consistent and comparable results to enhance the resolution of metabolite profiling and compound identification in young coconut samples to facilitate a deeper understanding of how their chemical components affect their physical, nutritional, and sensorial qualities.