In this paper we report the structural investigation of cysteine and glutathione capped Ag nanoparticles (NPs) by means of transmission electron microscopy (TEM), synchrotron X-ray diffraction (XRD) and pair distribution function (PDF) analysis. The combined use of these probes allowed us to observe the presence of two crystal structures in the coated AgNPs, i.e., the cubic and the hexagonal crystal structures of Ag. In particular, it was possible to demonstrate that the coated AgNPs are a nanoscale phase separated system where the two phases coexist within the single grain. In addition, the relative bulk amount of the fcc and hcp phases has been estimated and a possible correlation with the capping agent proposed.