Algae, despite being labeled as an underexplored biological source of chemical constituents, remain inadequately studied in terms of their metabolism. Metabolomics emerges as a high-throughput technology to investigate the full metabolic profile of samples that could aid in the understanding and characterization of algae. By delving into their primary composition, particularly for polysaccharides and phycobiliproteins, alongside secondary metabolites like polyphenols and pigments, researchers can uncover not only their rheological and nutritional properties but also their diverse biological activities. Given the growing interest in algae for food and related industries, innovative approaches should be explored to enhance the value of their functional components. In this sense, in the context of contemporary in silico studies, metabolomics should be paired with computational methodologies to develop novel techniques for studying biomolecular interactions. Molecular docking arises to predict the atomic-level interaction between a small molecule (ligands) and target proteins (proteins). This synergistic approach integrating both technologies could allow us to characterize algae profiles, evaluate their potential bioactive properties, and better understand their metabolism. This work pays attention to the metabolomic and computational strategies to be developed, which are aimed at the functional characterization of algae. By harnessing these technologies, we can unlock new possibilities for using algae in various industrial applications, paving the way for sustainable and innovative solutions in the future.