The fundamental understanding of the detailed relationship between molecular structure and material function remains a challenging task, until now. In order to understand the relative contribution of aromatic moieties and hydrophobicity of amino acid chains, we designed a library of ultrashort amyloid-like peptides based on Ar-Phe-X (where "Ar" represents different aromatic moieties and "X" represents amino acids having varied side-chain functionalities). Our research clearly indicated that the alteration in the size and hydrophobicity of the aromatic capping play a crucial role compared to the subtle change in the amino acid sequence of the dipeptide in dictating the final self-assembled structure and properties of these short peptide amphiphiles. Further, we explored our detailed understanding toward the controlled synthesis of bioinspired organic-inorganic hybrids. For the first time, we established the differential role of aliphatic and aromatic hydroxyl moieties toward the in situ shape-controlled synthesis of gold nanoparticles in three-dimensional nanostructures of hydrogels. To the best of our knowledge, it is the first report which demonstrated the formation of rectangular platonic gold nanoparticles using simple dipeptide hydrogels, exhibiting pH-dependent size control. Our study shows promising implications in bottom-up nanofabrication of next-generation nanomaterials with emergent properties.