Photodynamic therapy (PDT) is a promising treatment against multiantibiotic-resistant bacteria with the advantage of a low tendency towards antibiotic resistance. Due to their high PDT efficiencies and superior chemical stabilities, fullerenes have been proposed as effective photosensitizers for the photodynamic inactivation of bacteria. However, the biomedical applications of fullerenes are hindered by their limited aqueous solubility and apparent tendency to undergo aggregation. Herein, we report a hybrid supramolecular hydrogel prepared by the peptide-modulated self-assembly of fullerenes for targeted and sustained photodynamic antibacterial therapy. Aggregation of the fullerene in the hydrogel is largely inhibited through the non-covalent interactions between the peptide and the fullerene. Consequently, the PDT efficiency of the peptide-fullerene hydrogel is highly improved as compared to the untreated fullerene. The incorporation of fullerene profoundly improves the mechanical properties of the hydrogel, making the peptide-fullerene hydrogel a better injectable formulation for biomedical applications. In vitro and in vivo antibacterial results indicate that the peptide-fullerene hydrogels can effectively inhibit multiantibiotic-resistant Staphylococcus aureus and promote wound healing. This study offers a promising paradigm to adapt self-assembling small peptides with integration of multiple functions for biomedical applications.