Algae, a diverse group of photosynthetic organisms, are rich sources of secondary metabolites with various high-value bioactive compounds and properties. Algae profiling has gained significant importance due to its varied applications across the food, agricultural, pharmaceutical, cosmetic, bioenergy, and nutraceutical sectors. Despite their immense potential, algae’s biochemical complexity challenges their characterization and utilization. Metabolomics, encompassing targeted and untargeted approaches, offers a powerful lens to unravel these complexities, providing insights into algal physiology, stress responses, genes, metabolic pathways, and adaptations. The application of advanced analytical technologies, such as liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR), among others, has significantly enhanced the scope and precision of algal metabolomics. By leveraging these tools in algal research, untargeted metabolomics enables the unbiased profiling of metabolites, offering a comprehensive snapshot of the metabolic state and metabolite relationships. In contrast, targeted approaches provide a detailed quantification of specific metabolites of interest, such as lipids, carbohydrates, or pigments, needed for industrial applications. However, challenges persist in algae characterization, including the complexity of algal metabolomes, the standardization of protocols, high technological equipment, and the need for robust bioinformatics tools to handle large datasets. Therefore, this chapter provides an overview of targeted and untargeted metabolomics techniques in algal research, highlighting their principles, methodologies, and recent advancements in analytical technologies. Furthermore, the chapter examines the integration of metabolomics with other omics tools, offering insights into their role in characterizing algae and addressing current challenges. Ultimately, the major applications of these approaches in biotechnology, such as biofuel production, bioremediation, and the development of high-value algal products, will be emphasized while proposing future directions to overcome existing limitations in the field.