We employ molecular dynamics (MD) and time-dependent density functional theory (TDDFT) to explore the fluorescence of hydrogen-bonded dimer and trimer structures of cyclic FF (Phe-Phe) molecules. We show that in some of these configurations a photon can induce either an intra-molecular proton transfer, or an inter-molecular proton transfer that can occur in the excited S1 and S2 states. This proton transfer, taking place within the hydrogen bond, leads to a significant red-shift that can explain the experimentally observed visible fluorescence in biological and bioinspired peptide nanostructures with a β-sheet biomolecular arrangement. Finally, we also show that such proton transfer is highly sensitive to the geometrical bonding of the dimers and trimers and that it occurs only in specific configurations allowed by the formation of hydrogen bonds.