The interaction of cysteine molecules with the Si(111)-root 3x root 3-Ag surface has been investigated over the submonolayer to multilayer regime using X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations. With both upper step and lower step terraces, step edges, and antiphase boundaries, the root 3x root 3-Ag overlayer supported on Si(111) provides a rich two-dimensional template for studying site-specific biomolecular interactions. As an amino acid with three functional groups, cysteine is found to chemisorb through S-H bond cleavage and S-Ag bond linkage first at step edges and antiphase boundaries followed by island formation and expanded growth onto terraces. Intermolecular interactions are dominated by zwitterionic hydrogen bonding at higher coverages, producing a porous unordered interfacial layer composed of cysteine agglomerates at room temperature. Upon annealing, cysteine adsorbates induce structural transformation of the uniform root 3x root 3-Ag reconstructed surface lattice into metallic Ag clusters with a narrow size distribution and short-range ordering. Preferential nanoaggregate formation of cysteine at defect sites and c-ysteine-induced metal cluster formation promise a new approach to fabricating nanoclusters for potential applications in chemical sensing and catalysis.