Cyanobacteria are oxygenic prokaryotes that show both immense biological and chemical diversity. These ancient organisms are present in almost every type of habitat on Earth. They are a source of numerous natural products (NPs) that have significant ecological functions and biotechnological and nutritional benefits. The study of cyanobacterial metabolites has benefited from developments in bioinformatics and analytical instruments used in metabolomic investigations. This chapter examines a few studies that demonstrate the application of both targeted and untargeted metabolomics to the study of cyanobacteria’s NPs. To develop operative engineering solutions for growth enhancement, photosynthetic efficiency, and increased production, a deeper understanding of carbon/nitrogen metabolism, genetic regulation, route flux distribution, and integrative studies pertaining to the targeted biochemicals is needed. To present the state of knowledge regarding cyanobacterial metabolism, this chapter highlights the latest developments of genome-scale metabolic models (GSMMs), metabolomic analysis, and integrative modeling techniques.