The structurally rigid dipeptide Pro‐Pro, known to self assembled into well defined dumbbells followed by robust three dimensional copper embedded discs under the appropriate physicochemical conditions. Now the assembly of dipeptide Pro‐Pro in the presence of Ag(I) and Au(III) metal ions was studied followed by its application as potential antibacterial agents. In the presence of Au(III) ions, ordered two dimensional sheets of submicron dimensions were obtained whereas in the presence of Ag(I) ions mostly random aggregates were found. Microscopy and spectroscopic study revealed that the Pro‐Pro‐Au(III) structures, in essence, can be considered as toxic metal ion “reservoirs“ and can provide batter platform to target bacterial membrane. The antibacterial assay demonstrated that owing to high biocompatibility Pro‐Pro dipeptide with bacterial cell, this simplest dipeptide worked as metal ion delivery agent and therefore it can show great potential in locally addressing bacterial infections.