High spatial-resolution secondary ion microprobe spectrometry, synchrotron radiation Fourier-transform infrared spectroscopy and polyacrylamide gel analysis demonstrate the intimate association of proteins with spheroidal aggregates of biogenic zinc sulfide nanocrystals, an example of extracellular biomineralization. Experiments involving synthetic ZnS nanoparticles and representative amino acids indicate a driving role for cysteine in rapid nanoparticle aggregation. These findings suggest that microbially-derived extracellular proteins can limit dispersal of nanoparticulate metal-bearing phases, such as the mineral products of bioremediation, that may otherwise be transported away from their source by subsurface fluid flow.