Nanoparticles synthesis under green conditions has been performed using natural resources to diminish the use of toxic chemicals. For instance, microbial synthesis has allowed to produce nanoparticles that are biocompatible, stable, and safe. Microorganisms allow crystal growth and prevent aggregation. Microorganisms act as reducing and capping agents because microorganisms provide enzymes, peptides, poly(amino acids), polyhydroxyalkanoate, and polysaccharides. Here, we review microorganisms-based synthesis of nanoparticles containing gold, silver, platinum, palladium, copper, titanium dioxide, zinc oxide, iron oxide, and selenium. The size of nanoparticles ranges generally from 1 to 100 nm with spherical, rod shape, triangular, cube, and hexagonal shapes. We present nanoparticle properties and applications in waste treatment, cancer treatment, antibacterial, antimicrobial, antifungal, and antioxidants.