To realize the add value of protein resources from mung bean processing by-products, mung bean peptides-zinc chelate (MBP-Zn), a novel zinc supplement, was synthesized in the present study. Under the optimized process conditions (MBP concentration of 6%, pH 5.0, mass ratio of MBP to zinc salt of 2:1, temperature of 60 °C and time of 80 min), the zinc chelation rate of MBP-Zn reached up to 98.15%. Integrating the results of Fourier transform infrared spectroscopy and amino acid profiles, it is inferred that zinc ions may bind to MBP via carboxy oxygen, amino nitrogen, and sulfhydryl sulfur atoms. The incorporation of zinc ions dramatically changed the structure of the chelate, as evidenced by the blue shift and attenuation of the original UV and fluorescence spectra. The morphological analysis revealed that Zn2+ induced cross-linking of peptides, forming enlarged nanoparticles that fragmented the original smooth surface of MBP. Surprisingly, the superior stability of MBP-Zn over the conventional zinc supplement ZnSO4 was confirmed, regardless of pH and temperature variations, or simulated gastrointestinal digestion circumstances. These findings pave the way for the large-scale production of mung bean peptide-based zinc supplements as nutraceuticals in the food industry.