Quantum dots (QDs) are semiconductor materials that range from 2 to 10 nanometers. These nanomaterials (NMs) are smaller and have more unique properties compared to conventional nanoparticles (NPs). One of the unique properties of QDs is their special optoelectronic properties, making it possible to apply these NMs in bioimaging. Different size and shape QDs, which are used in various fields such as bioimaging, biosensing, cancer therapy, and drug delivery, have so far been produced by chemical methods. However, chemical synthesis provides expensive routes and causes serious environmental and health issues. Therefore, various biological systems such as bacteria, fungi, yeasts, algae, and plants are considered as potent eco-friendly green nanofactories for the biosynthesis of QDs, which are both economic and environmentally safe. The review aims to provide a descriptive overview of the various microbial agents for the synthesis of QDs and their biomedical applications for the diagnosis and treatment of cancer and SARS-CoV-2.