Supramolecular fibers assembled from peptide amphiphiles are promising materials for the delivery of biopharmaceuticals. However, strategies for directly conjugating folded proteins onto these supramolecular dynamic assemblies remain limited. Herein, we demonstrate that aromatic peptide amphiphiles that integrate self-assembly motifs with enzymatic recognition sequences enable the synthesis of supramolecular fibrous materials amenable to protein conjugation in their native folded state. The designed peptide amphiphiles self-assembled into fibers through a combination of hydrophobic, aromatic, and hydrogen bonding interactions in aqueous media. Using microbial transglutaminase, a recombinant enhanced green fluorescent protein (EGFP), used as a model proteinaceous antigen, was covalently coupled to the fibers via site-specific enzymatic cross-linking. This direct conjugation greatly enhanced the intracellular delivery of EGFP to murine dendritic cells in a manner dependent upon the peptide design. Notably, the resulting conjugates exhibited markedly increased immunogenicity compared to the protein alone, as evidenced by the elevated production of antigen-specific immunoglobulin G. These findings position the conjugated supramolecular fibers as a versatile platform for protein delivery and vaccine development.