This study convincingly demonstrates a unique example of the self-assembly of a naphthalene diimide (NDI)-appended peptide into a fluorescent J-aggregate in aqueous media. Moreover, this aggregated species shows a remarkable yellow fluorescence in solid state, an unusual phenomenon for NDI-based compounds. The aggregated species has been characterized using transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy, X-ray diffraction, time-correlated single proton counting (TCSPC), UV–vis, and photoluminescence studies. TEM images reveal cross-linked nanofibrillar morphology of this aggregated species in water (pH 7.4). TCSPC study clearly indicates that the aggregated species in water has a higher average lifetime compared to that of the non-aggregated species. Interestingly, this NDI-based peptide shows H⁺ ion concentration-dependent change in the emission property in water. The fluorescence output is erased completely in the presence of an alkali, and it reappears in the presence of an acid, indicating its erasing and rewritable property. This indicates its probable use in authentication tools for security purposes as a rewritable fluorescence color code. This NDI-appended peptide-based molecule can be used for encryption of information due to erasing and rewritable property of the molecule in the aggregated state in aqueous medium.