Microorganisms produce complex biomolecules with unique properties to help them survive in unfavorable environmental conditions. Secondary metabolites are natural products, produced by a wide range of bacteria, cyanobacteria, fungi, and microalgae. These natural products are rich in various biologically active molecules with varying chemical structures and possess antimicrobial, anticancer, and anti-inflammatory properties. Many of these compounds have been developed into potential therapeutics for human diseases and have found applications in relevant industries. This book chapter provides a detailed overview of past and ongoing studies with reports of promising microorganisms which can serve as cell factories to generate biologically active molecules.