A clear description of how surface morphology is affected by the bonding of biomolecules with metal surfaces is critical to identify due to the potential applications in microelectronics, medical devices, and biosensors. Amino acids (AAs) on bare Au(111) were previously observed to trap Au adatoms, eventually leading to the formation of one atom high metal islands. To better understand the role of surface identity, L-isoleucine on Au(111) modified with a Ag thin film was investigated at ambient conditions with electrochemical scanning tunneling microscopy. The mere presence of an Ag monolayer drastically changed the amino acid/surface interactions despite the chemical similarity of Au and Ag. The adsorption of the AAs on the Ag monolayer drastically altered the surface and caused significant surface roughening distinct from 2D growth which had previously existed only on top of the surface. This roughening occurred layer-by-layer and was not restricted to the first layer of the surface as seen with sulfur containing molecules. Notably, this study demonstrates surface roughening that is occurring under extremely mild conditions highlighting the ability of Ag thin films to markedly alter surface chemistry in concert with biomolecules.