In solvent extraction, the self-assembly of amphiphilic molecules into an organized structure is the phenomenon responsible for the transfer of the metal ion from the aqueous phase to the organic solvent. Despite their significance for chemical engineering and separation science, the forces driving the solute transfer are not fully understood. Instead of assuming the simple complexation reaction with predefined stoichiometry, we model synergistic extraction systems by a colloidal approach that explicitly takes into account the self-assembly resulting from the amphiphilic nature of the extractants. Contrary to the current paradigm of simple stoichiometry behind liquid–liquid extraction, there is a severe polydispersity of aggregates completely different in compositions, but similar in the free energy. This variety of structures on the nanoscale is responsible for the synergistic transfer of ions to the organic phase. Synergy can be understood as a reciprocal effect of chelation: it enhances extraction because it increases the configurational entropy of an extracted ion. The global overview of the complex nature of a synergistic mixture shows different regimes in self-assembly, and thus in the extraction efficiency, which can be tuned with respect to the green chemistry aspect.