We highlight the structural diversity of strategically designed two short peptide amphiphiles (sPAs) and describe their structure–function relationship studies. The shuffling of two key amino acids, that is, tyrosine and phenylalanine, in a designed sPA lead to a pair of constitutional isomers. Such small and strategic alteration can bring a substantial change in the self‐assembling pattern. Inspired from the naturally occurring metallopeptides, bioactive transition‐metal ions were used for constructing the unusual nanostructures. Use of appropriate metal ions created bigger differences between the properties of these isomers and hence the self‐assembly. Coordination of appropriate transition metal ions modifies the internal nanoscale structures of sPA, thus leading to the formation of vertically stacked terraced layers with decreasing size, which possess a high degree of dimensional regularity. We propose that such metal‐induced terraced nanodome‐like hierarchical self‐assembly may have relevance for specific biotechnology applications.