Quantum dots (QDs) are fluorescent nanocrystals with superb photo-physical properties. Applications of QDs have been exponentially increased during the past decade. They can be employed in several disciplines, including biological, optical, biomedical, engineering, and energy applications. This review highlights the structural composition and distinctive features of QDs, such as resistance to photo-bleaching, wide range of excitations, and size-dependent light emission features. Physical and chemical preparation of QDs have prominent downsides, including high costs, regeneration of hazardous byproducts, and use of external noxious chemicals for capping and stabilization purposes. To eliminate the demerits of these methods, an emphasis on the latest progress of microbial synthesis of QDs by bacteria, yeast, and fungi is introduced. Some of the biomedical applications of QDs are overviewed as well, such as tumor and microRNA detection, drug delivery, photodynamic therapy, and microbial labeling. Challenges facing the microbial fabrication of QDs are discussed with the future prospects to fully maximize the yield of QDs by elucidating the key enzymes intermediating the nucleation and growth of QDs. Exploration of the distribution and mode of action of QDs is required to promote their biomedical applications.