Supramolecular organization of amphiphilic extractant molecules is involved in metal cation selectivity and separation kinetics during solvent extraction. The relationship between extractant associates/aggregates formed in the organic bulk phase and at the liquid–liquid interface is poorly understood even though it affects the extraction mechanism. The nanoscopic structures of the extraction systems N,N,N′,N′-tetrahexylmalonamide (THMA) in toluene and N,N′-dibutyl-N,N′-dimethyl-2-tetradecylmalonamide (DBMA) in n-heptane, used for either Pd(II) or Nd(III) selective extraction from an acidic aqueous phase, were examined. These systems present markedly different affinity for Pd(II) and Nd(III), and extraction kinetics. Extractant organization in the organic bulk phase and at the interface were compared by small-angle X-ray scattering, interfacial tension, and neutron reflectivity. THMA in toluene forms small associates in the organic bulk phase and accumulates in a diffuse layer at the interface, decreasing Pd(II) coordination probability and resulting in slow extraction. DBMA in n-heptane forms large aggregates and a compact, dense interfacial layer, resulting in rapid Pd(II) and Nd(III) extraction. Thus, Pd(II) extraction is driven by interfacial coordination alone, whereas the incorporation of Nd(III) into the core of large aggregates governs Nd(III) extraction in the interfacial layer. These results suggest that the interface should be described as a nanoscale interphase containing a high extractant concentration compared with the organic bulk phase.