The use of Cold Atmospheric Pressure Plasma (CAPP) technology in the production of peptide-based materials has shown great potential in modern technology. Herein, two aggregation-prone oligopeptides, GNNQQNY and KLVFFA, were subjected to CAPP treatment to form supramolecular assemblies/aggregates. Through peptide engineering and biophysical techniques, the effect of CAPP-generated reactive oxygen and nitrogen species (ROS/RNS) on the oligopeptides were investigated for different treatment times revealing that the formation of these aggregates were primarily driven by electrostatic interactions without any chemical modifications. Field Emission-Scanning Electron Microscopy (FE-SEM) and Thioflavin T (ThT) binding assay confirmed the presence of distinct β-strands, particularly in the aggregates of the KLVFFA peptide upon CAPP irradiation. The combination of CAPP technology with peptide self-assembly process and the characterization techniques employed in this study holds promise for the development of such peptide supramolecular structures based on the specific amino acid sequences.