Self-assembled peptide amphiphile (PA) nanofibers have emerged as bio-inspired materials with numerous applications in nanotechnology. However, environmental variables, such as salt concentration, pH, or temperature, can greatly impact the self-assembly process. Being able to tune the electrostatic interaction and intermolecular hydrogen bonding is essential in designing stable structures. The ion-specific effects on stabilization of peptides in solution typically follow the Hofmeister series and can be used to control the strength of interaction between ions and PAs. In this study, we performed atomistic molecular dynamics simulations to understand how we can use Hofmeister effects to control PA nanofiber structure. Our results show that the formation of β-sheets in PA nanofibers follows a direct Hofmeister order (F- > Cl- > Br- > I-), resulting from the strong interaction of strongly hydrated ions (F-, Cl-) with the charged amino acid residues on the nanofiber surface. On the other hand, weakly hydrated ions (I-, Br-) interact more preferably with the hydrophobic residues that form the stable β-sheets in the interior of the peptide closer to the core of the nanofiber. We also found that strongly hydrated ions can induce coil to β-sheet transition in the lysine residues close to the nanofiber surface by forming salt bridges between lysine residues of neighboring PA chains. With this work, we provide insight into how the structure of PA nanofibers can be tuned using different salt solutions for developing more stable supramolecular nanofibers for future applications.