Supramolecular bioinspired peptide nanostructures are considered as a new frontier in materials science and engineering. The nano‐crystalline packing of various peptide nanostructures, and especially those lacking a center of symmetry at the nanoscale, give rise to exceptional physical properties. Specifically, native aromatic diphenylalanine (FF) and aliphatic dileucine (LL) based nanotubes, which are related to hexagonal and orthorhombic non‐centrosymmetric crystalline groups respectively, exhibit fundamental physical phenomena, such as piezoelectricity and second harmonic generation (SHG). This review covers our latest findings on the physical properties of FF and LL nanostructures. We show that heat treatment at the temperature range of 140–180 °C induces irreversible phase transition in FF and LL nanotubes, wherein all their physical properties and structure at all levels (molecular, electronic, optical, space symmetry, morphology, wettability) change. Using high resolution microscopy tools, based on Kelvin probe force microscopy (KPFM), piezoresponse force microscopy (PFM), and SHG, as well as Raman spectroscopy, we demonstrate that the phase‐transition phenomena in FF and LL nanotubes leads to full reconstruction and reassembling of native open‐end nanotubes into new fiber‐like structures, followed by deep variation of non‐centrosymmetric to centrosymmetric space symmetry. As a result, the newly generated centrosymmetric phase in FF and LL nanostructures demonstrates neither piezoelectric effect nor nonlinear optical activity.