Coffee contains numerous both nonvolatile and volatile compounds, which contribute to its widely known flavor and aroma. Therefore, analyzing the composition of these compounds is essential for coffee quality research and enhancing the understanding of their roles in coffee quality. The metabolomics approach provides metabolite profiling, covering a wide range of compounds, and has become a common method in coffee research. The chapter details the gas chromatography-mass spectrometry (GC-MS)-based metabolomics workflow used to analyze both nonvolatile and volatile compounds in coffee. Two separate subchapters are provided to focus on the specific methodologies for sample preparation, extraction, and derivatization needed for each compound type.