Thermally induced phase transformation in bioorganic nanotubes, which self‐assembled from two ultrashort dipeptides of different origin, aromatic diphenylalanine (FF) and aliphatic dileucine (LL), is studied. In both FF and LL nanotubes, irreversible phase transformation found at 120–180 °C is governed by linear‐to‐cyclic dipeptide molecular modification followed by formation of extended β‐sheet structure. As a result of this process, native open‐end FF and LL nanotubes are transformed into ultrathin nanofibrils. Found deep reconstructions at all levels from macroscopic (morphology) and structural space symmetry to molecular give rise to new optical properties in both aromatic FF and aliphatic LL nanofibrils and generation of blue photoluminescence (PL) emission. It is shown that observed blue PL peak is similar in these supramolecular nanofibrillar structures and is excited by the network of non‐covalent hydrogen bonds that link newly thermally induced neighboring cyclic dipeptide strands to final extended β‐sheet structure of amyloid‐like nanofibrils. The observed blue PL peak in short dipeptide nanofibrils is similar to the blue PL peak that was recently found in amyloid fibrils and can be considered as the optical signature of β‐sheet structures. Nanotubular structures were characterized by environmental scanning electron microscope, ToF‐secondary ion mass spectroscopy, CD and fluorescence spectroscopy. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.