Pectin was extracted from Citrus sinensis fruit peel, an agro-waste material, by an acid-assisted method, and the percentage of pectin extracted was 26.8%. The extracted pectin was then modified by ionic cross-linking of Cu²⁺ and Zn²⁺ ions with the pectin to form metal-pectin complexes by a controlled coordination method. The structure of the modified pectin complexes was studied by FT-IR, XRD, SEM, and EDX techniques. The coordination of metal ions with the carboxylate functional group of the pectin backbone was confirmed by the shifting of the characteristic peaks in the FT-IR spectra. The amorphous nature of the pectin backbone remained unchanged after modification, as evidenced by the XRD patterns. The morphology of the pectin changes from flakes to aggregated form, as evidenced by the SEM images. The presence of metal ions in the complexes was confirmed by the EDX technique. Swelling and pH stability tests have shown reduced swelling potential and increased structural stability of the metal-pectin complexes, especially at neutral pH, which is attributed to the formation of a cross-linked ionic network. In addition, the metal-modified pectin material has shown increased antimicrobial potential compared to the native material. This is a testament to the role of transition metals in enhancing the bio functional potential of materials. In conclusion, the present work provides an efficient and sustainable strategy for the valorization of citrus waste materials for various potential applications.