Solvent molecules significantly affect the supramolecular self-assembly, for example, in forming solvent-bridged hydrogen bonding networks. Even small changes in solvent composition can have dramatic impact on supramolecular assembly. Herein, we demonstrate the use of trace solvents (as low as 0.04%) to tune the morphology and consequent functions of supramolecular nanostructures based on an aromatic peptide bola-amphiphile. Specifically, perylene bisimide-(di)glycine-tyrosine (PBI-[GY](2)) bola-amphiphile was shown to give rise to red-emitting nanofibers when assembled in water, while exposure to trace organic solvents such as tetrahydrofuran (THF) and others via solvent-evaporation followed by aqueous assembly gave rise to white-light-emitting nanospheres. Differential hydrogen bonding between water (donor and acceptor) and THF (acceptor only) impacts supramolecular organization, which was verified using a density functional theory (DFT) simulation. The tunable consequent surface hydrophobicity was utilized in staining the cytoplasm and membrane of cells, respectively. The trace-solvent effect achieved through evaporationdissolution provides a methodology to mediate the morphologies and consequent functions for supramolecular biomaterials controlled by the self-assembly pathway.