The world population is expected to increase up to 9.6 billion by 2050. This triggers the demand for food security and its nutritional value. Despite the advancements in the field of medicine, current research focuses on investigating natural‐origin functional foods with tremendous health‐supporting properties. It includes various natural sources such as animals, plants, algae, fungi, and bacteria. The Algae group is still under investigation to find the best alternative to other previously explored sources. Algae possess remarkable potential for synthesizing natural metabolites, including primary metabolites (polysaccharides, proteins, and lipids) and secondary metabolites (Flavonoids, bromophenols, phenolic compounds, and polyphenols). These bioactive compounds have enormous anticancer, antimicrobial, and neuroprotection applications. This provokes researcher interest in exploring algae strains to optimize their metabolite production to utilize them as a functional food. Metabolomics techniques can be utilized to investigate biological samples. It will create new ways to explore algae strains that have not yet been investigated. A closed pond cultivation system is attractive to enhance algae growth in highly controlled conditions. This review emphasizes algae metabolism, cultivation methods, metabolomics analysis, genetic engineering, and advanced genome editing tools such as the CRISPR CAS9 system, which can be utilized to manipulate the algae genome for increased production.