The mechanical properties of self-assembled fibrillar networks are influenced by the specific intermolecular interactions that modulate fiber entanglements. We investigate how changing these interactions influences the mechanics of self-assembled nanofiber gels composed of peptide amphiphile (PA) molecules. PAs developed in our laboratory self assemble into gels of nanofibers after neutralization or salt-mediated screening of the charged residues in their peptide segment. We report here on the gelation, stiffness, and response to deformation of gels formed from a negatively charged PA and HCl or CaCl2. Scanning electron microscopy of these gels demonstrates a similar morphology, whereas the oscillatory rheological measurements indicate that the calcium-mediated ionic bridges in CaCl2-PA gels form stronger intra- and interfiber cross-links than the hydrogen bonds formed by the protonated carboxylic acid residues in HCl-PA gels. As a result, CaCl2-PA gels can withstand higher strains than HCl-PA gels. After exposure to a series of strain sweeps with increasing strain amplitude HCl- and CaCl2-PA gels both recover 42% of their original stiffness. In contrast, after sustained deformation at 100% strain, HCl-PA gels recover nearly 90% of their original stiffness after 10 min, while the CaCl2-PA gels only recover 35%. This result suggests that the hydrogen bonds formed by the protonated acids in the HCl-PA gels allow the gel to relax quickly to its initial state, while the strong calcium cross-links in the CaCl2-PA gels lock in the deformed structure and inhibit the gel's ability to recover. We also show that the rheological scaling behaviors of HCl-and CaCl2-PA gels are consistent with that of uncross- and cross-linked semiflexible biopolymer networks, respectively. The ability to modify how self-assembled fibrillar networks respond to deformations is important in developing self-assembled gels that can resist and recover from the large deformations that these gels encounter while serving as synthetic cell scaffolds in vivo.