Quantum confined (QC) materials have been extensively studied for imaging and quantum information applications. Due to intrinsic limitations of low biocompatibility and challenging modulation, conventional metal-based inorganic QC photoluminescent materials face critical bottlenecks in bio-imaging and bio-machine interface applications. Here, we report aromatic cyclo-dipeptides dimerize into quantum dots, which serve as building blocks to further self-assemble into QC supramolecular structures with diverse morphologies and photoluminescence properties. In particular, the emission could be tuned from the visible to the near-infrared region (420 nm to 820 nm) by modulating the self-assembling process, via coordination with Zn(II), substitution with D-type enantiomers, oxidation by Cu(II) or UV irradiation, and replacement of the solvent or side-chain aromatic moieties. Moreover, no cytotoxic effect was observed for these nanostructures, and their ability to serve for in vivo imaging and as phosphors for light emitting diodes was demonstrated. The results reveal that the morphologies and optical properties of the aromatic cyclo-dipeptides self-assemblies can be tuned, making them potential candidates for supramolecular QC materials providing biocompatible alternatives for broad biological and biomedical applications.