Metal-infiltrated protein crystals form a novel class of bio-nanomaterials of great interest for applications in biomedicine, chemistry, and optoelectronics. As yet, very little is known about the internal structure of these materials and the interconnectivity of the metallic network. Here, the optical response of individual Au- and Ag-infiltrated cross-linked lysozyme crystals is investigated using angle- and polarization-dependent spectroscopy. The measurements unequivocally show that metallic inclusions formed inside the nanoporous solvent channels do not connect into continuous nanowires, but rather consist of ensembles of isolated spheroidal nanoclusters with aspect ratios as high as a value of four, and which exhibit a pronounced plasmonic response that is isotropic on a macroscopic length scale. Fluorescence measurement in the visible range show a strong contribution from the protein host, which is quenched by the Au inclusions, and a weaker contribution attributed to the molecule-like emission from small Au-clusters.