The synthesis of metal and semiconductor nanoparticles and nanostructures has seen a tremendous advancement in the field of nanomaterials research owing to their high optical, electrical, catalytic and photocatalytic properties. To date, a number of methods have been reported for the synthesis of nanoparticles, however, they typically require costly and hazardous chemicals and do not usually produce particles of high yields and uniform sizes and monodispersity. Hence, there still remains a need to develop cost-efficient and greener means of synthesizing nanostructures at an industrial scale. As such, we aim to utilize the machinery of biological organisms in biologically synthesizing nanoscale materials with great control over their size and shape to design innovative bionanomanufacturing platforms that will enable reproducible and large-scale synthesis of metal nanostructures with uniform size, shape and high purity. Herein, we demonstrate the in situ microbial synthesis of silver (Ag) and gold (Au) nanoparticles using the cell filtrates of Rhodobacter sphaeroides, Rhodobacter capsulatus, and Bacillus subtilis, which resulted in spherical nanoparticles with uniform sizes (5 ~ 20 nm) and monodispersity. We studied the effect of incubation time and metal ion concentration on the growth and size of the particles, and our data indicate that there is a linear relationship between the particle size, incubation time and metal ion concentration. We also performed preliminary screening of the proteins responsible for the nanoparticle biosynthesis by carrying out enzyme inhibition studies and proteomics analysis of the cell filtrates. Our initial results provide insights into the mechanism of biological nanoparticle synthesis, and thus, lay the groundwork for the isolation of the active proteins and translation into in vitro and cell-free, protein-based nanofabrication techniques, which offer great avenues for both fundamental and applied nanomaterials research.