The latest trend in the field of nanotechnology is the adoption of novel green technologies by utilizing microorganisms as “microbial cell factories” in the production of nanoparticles. In recent years, microorganisms, including bacteria, fungi, and microalgae, have been widely explored for the intracellular/extracellular synthesis of nanoparticles. Remarkably, scaled-up production of nanoparticles via biogenic synthesis is an eco-friendly approach resulting in less/non-toxic nanomaterials, without any necessity of toxic/hazardous chemicals and high pressure/temperature process conditions used in conventional methods. Hence, microbial nanoparticles are mainly preferred in the fields of biomedical and pharmaceutical for diverse applications including but not limited to, drug delivery systems, antimicrobials, tissue regenerative biomaterials, biosensors, and bioimaging. In accordance, the chapter holistically focuses on the various types of microorganisms used for nanoparticle production and their potential in real-world applications. Also, the challenges and limitations associated with the scaled-up production of biogenic nanoparticles, and potential solutions are discussed, to distinguish the scope of future research enhancing the economic feasibility and sustainability.