Efficient and selective extractions of precious and critical metal ions such as Au(III) and Pd(II) were investigated using zirconia nanoparticles surface modified with different organic mono- and di-carbamoyl phosphonic acid ligands. The modification is made on the surface of commercial ZrO2 that is dispersed in aqueous suspension and was achieved by optimizing the Bronsted acid–base reaction in ethanol/H2O solution (1:2), resulting in inorganic–organic systems of ZrO2-Ln (Ln: organic carbamoyl phosphonic acid ligand). The presence, binding, amount, and stability of the organic ligand on the surface of zirconia nanoparticles were confirmed by different characterizations such as TGA, BET, ATR-FTIR, and 31P-NMR. Characterizations showed that all the prepared modified zirconia had a similar specific surface area (50 m2.g−1) and the same amount of ligand on the zirconia surface in a 1:50 molar ratio. ATR-FTIR and 31P-NMR data were used to elucidate the most favorable binding mode. Batch adsorption results showed that (i) ZrO2 surface modified with di-carbamoyl phosphonic acid ligands had the highest adsorption efficiency to extract metals than mono-carbamoyl ligands, and (ii) higher hydrophobicity of the ligand led to better adsorption efficiency. The surface-modified ZrO2 with di-N,N-butyl carbamoyl pentyl phosphonic acid ligand (ZrO2-L6) showed promising stability, efficiency, and reusability in industrial applications for selective gold recovery. In terms of thermodynamic and kinetic adsorption data, ZrO2-L6 fits the Langmuir adsorption model and pseudo-second-order kinetic model for the adsorption of Au(III) with maximum experimental adsorption capacity qmax = 6.4 mg.g−1.