The chapter explores the metabolites, molecular diversity, and application of cyanobacteria in the beverage sector. Information in the chapter was compiled from 79 scientific publications based on a thorough literature search using keywords such as “cyanobacteria,” “metabolites,” “blue-green algae,” “beverage applications,” and in scientific databases such as Google Scholar, Science Direct, PubMed, and Medicine. While the chapter identified numerous metabolites from various cyanobacteria genera and species, five classes of secondary metabolites such as alkaloids, terpenoids, ribosomal peptides, non-ribosomal peptides, and polyketides with prominent members of these classes not limited to vinblastine, ephedrine, galantamine, vincamine, quinidine, piperine, geosmin, zeaxanthin, canthaxanthin, echinenone, myxoxanthophyll, β-carotene, microcystin, apratoxin, lyngbyatoxin, and aplysiatoxin have been established. The chapter also reveals that, despite the different habitats for the existence of this important prokaryotic organism, little has been done to determine the microbial diversity’s structure and composition. Additionally, studies on its application in the beverage industry are limited, and this calls for dedicated attention to these gray areas to fully maximize the economic potential of this vital organism.