The instability of anthocyanin to environmental stressors severely limits its applications as a natural bioactive pigment. To overcome these limitations, this proof-of-concept study utilizes the high biocompatibility of peptide molecules and the unique gel microstructure to develop innovative peptide-based gels. Characterization of the gels was conducted through AFM, SEM, rheological analysis, and CD spectrum. These analyses confirmed the fibrous mesh structure and impressive mechanical strength of the peptide-based gels. The cytotoxicity evaluation using MTT and hemolysis analysis showed high biocompatibility. Encapsulation efficiency analysis and fluorescence microscopy images demonstrated successful and efficient encapsulation of anthocyanins in all four peptide-based gels, with uniform distribution. Moreover, systematic investigations were conducted to assess the impact of peptide-based gels on the stability of natural anthocyanins under environmental stressors such as temperature, pH variations, and exposure to metal ions. Notably, the results revealed a significant enhancement in stability, including improved long-term storage and antioxidant activity. In conclusion, this study successfully developed four novel peptide-based gels that effectively protect natural anthocyanins from environmental stressors, highlighting their potential in various fields such as food and biology.