Defatted soybean meal, walnut meal, cottonseed meal and wheat gluten flour were hydrolyzed with Alcalase to prepare vegetable protein hydrolysates (VPHs), respectively. Through ethanol fractionation, peptides with lower molecular weight and higher hydrophobicity were enriched in ethanol-soluble VPHs (VPHs-Es), and metal-binding content of VPHs-Es was significantly increased. Zinc and iron were much easier to combine with lower molecular weight peptides (MW < 1 kDa) than calcium. Comparably, ethanol-soluble soybean protein hydrolysates (SPH-Es) had a better metal-binding capacity. The Fourier transform infrared spectra and amino acid composition analysis revealed that the carboxyl oxygen and amino nitrogen were the main binding sites for chelating, and divalent metals had different chelating preferences. The molecular weight distribution, particle size and scanning electron microscope analysis demonstrated significant microstructural differences among the metal (Ca, Zn, Fe) chelates. In particular, obvious aggregation occurred in Ca-SPH-Es, which was induced by hydrogen bonding and electrostatic interaction. Moreover, the gastrointestinal stability of metal chelates was 71.48%, 90.70% and 85.60% for Ca-SPH-Es, Zn-SPH-Es and Fe-SPH-Es, respectively, thus providing a guidance for the exploration of organometallic supplements. Display omitted •Ethanol fractionation significantly increased the metal-binding content of ethanol-soluble peptides.•Hydrophobicity and molecular size of peptides greatly influenced the metal-binding capacity.•Calcium, zinc and iron had different chelating preferences with peptides.•Gastrointestinal stability of metal-SPH-Es was high.