While the ordering of amino acids in proteins and peptide-based materials is known to affect their folding patterns and supramolecular architectures, tailoring self-assembly behavior in stimuli responsive peptides by isomerizing a peptide sequence has not been extensively explored. Here, we show that changing the position of a single hydrophobic amino acid in short amphiphilic peptides can dramatically alter their pH-triggered self-assembly transitions. Using palmitoyl-IAAAEEEE-NH2 and palmitoyl-IAAAEEEEK(DO3A:Gd)-NH2 as controls, moving the Isoleucine away from the palmitoyl tail preferentially induces nanofiber formation over spherical micelles. Shifting the Isoleucine one residue away makes the transition pH more basic by 2 units. When in the third or fourth position, nanofibers are formed exclusively above 10 μM. We propose that moving the Isoleucine away from the tail enhances its ability to promote β-sheet formation instead of folding back into the palmitoyl core. These findings reveal a novel strategy for programming pH-triggered self-assembly by isomerizing a peptide sequence.