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Metal chelators and porous sorbents are two of the forefront technologies applied for the recovery and separation of hazardous and/or valuable metal ions from aqueous solutions (i.e., polluted water sources, metal-rich mining wastewaters, acid leachates, and so forth). The transfer of the metal coordination functions of metal chelators to chemically stable host materials had only limited success so far. Here, we report the installation of natural acids (i.e., malic acid, mercaptosuccinic acid, succinic acid, fumaric acid, and citric acid) and amino acids (i.e., histidine, cysteine, and asparagine) within a porous zirconium-based trimesate metal−organic framework (MOF), namely, MOF-808. Applying this strategy, we were able to produce a pore environment spatially decorated with multiple functional groups usually found in commercial chelator molecules. The chemical stability of the amino acid molecules installed by the solvent-assisted ligand exchange has been studied to delimitate the applicability window of these materials. The adsorption affinity of MOF-808@(amino)acids in static and column-bed configurations can be finetuned as a function of the amino acid residues installed in the framework. MOF-808(amino)acid columns can be applied efficiently both for water remediation of heavy metals and for the separation of metal ions with different acidities. For instance, the initial trends for the dispersion of rare-earth elements have been identified. Electron paramagnetic resonance and inelastic neutron scattering spectroscopy reveal that MOF-808@(amino)acids stabilize metal centers as isolated and clustered species in a coordination fashion that involves both the amine and thiol functionals and that affects the vibrational freedom of some of the chemical groups of the amino acid molecules. The metal-ion stabilization within amino acid-decorated MOFs opens the avenue for application for pseudo biocatalysis purposes in the near future.