Metabolomics is a powerful and rapidly evolving tool to unravel the complex biochemical nature of plants. Through this, the plant metabolome is continuously explored to understand plant physiology, stress responses, and the production of valuable secondary metabolites. This chapter provides a comprehensive overview of plant metabolomics, encompassing sample preparation strategies, extending to widely used analytical platforms such as capillary electrophoresis–mass spectrometry (CE–MS), gas chromatography–mass spectrometry (GC–MS), liquid chromatography–mass spectrometry (LC–MS), and nuclear magnetic resonance (NMR), as well as the typical workflow from data acquisition to bioinformatics-driven data analysis. This chapter also highlights the diverse applications of metabolomics in plant research, including studies relevant to plant development, stress response, crop improvement, and the discovery of bioactive compounds. Key challenges in plant metabolomics research, such as metabolite annotation, lack of standardized protocols, limited spectral libraries, and the complexity of the plant metabolome, are also discussed, along with emerging trends and future directions that continue to shape metabolomics as an indispensable tool in plant science research.