There is increasing interest in studying the interaction of nanoparticles with biomolecules, microorganisms, and noble metals to explore their unique properties and potential biological applications. The synthetic butyloxycarbonyl (Boc)‐protected methyl esters of peptides composed of only aliphatic amino acids (Boc‐Ile‐Ile‐OMe and Boc‐Leu‐Ile‐Ile‐OMe) self‐assembled into nanotubes and spheres, respectively, has been previously demonstrated. Herein, the characterization of these peptide nanoparticles incorporated with silver by means of various spectrometric methods and electron microscopy imaging techniques is described. The antibacterial activity of Ag‐doped nanoparticles was determined. These peptide nanoparticles were demonstrated to be useful encapsulants of charged fluorescent dyes. This investigation demonstrates the potential of these short peptide nanoparticles to design formulations of antimicrobial agents that will enhance their activity and as fluorescent probes for cell imaging.