Short- and long-range correlations between solutes in solvents can influence the macroscopic chemistry and physical properties of solutions in ways that are not fully understood. The class of liquids known as complex (structured) fluids—containing multiscale aggregates resulting from weak self-assembly—are especially important in energy-relevant systems employed for a variety of chemical- and biological-based purification, separation, and catalytic processes. In these, solute (mass) transfer across liquid–liquid (water, oil) phase boundaries is the core function. Oftentimes the operational success of phase transfer chemistry is dependent upon the bulk fluid structures for which a common functional motif and an archetype aggregate is the micelle. In particular, there is an emerging consensus that mass transfer and bulk organic phase behaviors—notably the critical phenomenon of phase splitting—are impacted by the effects of micellar-like aggregates in water-in-oil microemulsions. In this study, we elucidate the microscopic structures and mesoscopic architectures of metal-, water-, and acid-loaded organic phases using a combination of X-ray and neutron experimentation as well as density functional theory and molecular dynamics simulations. The key conclusion is that the transfer of metal ions between an aqueous phase and an organic one involves the formation of small mononuclear clusters typical of metal–ligand coordination chemistry, at one extreme, in the organic phase, and their aggregation to multinuclear primary clusters that self-assemble to form even larger superclusters typical of supramolecular chemistry, at the other. Our metrical results add an orthogonal perspective to the energetics-based view of phase splitting in chemical separations known as the micellar model—founded upon the interpretation of small-angle neutron scattering data—with respect to a more general phase-space (gas–liquid) model of soft matter self-assembly and particle growth. The structure hierarchy observed in the aggregation of our quinary (zirconium nitrate–nitric acid–water–tri-n-butyl phosphate–n-octane) system is relevant to understanding solution phase transitions, in general, and the function of engineered fluids with metalloamphiphiles, in particular, for mass transfer applications, such as demixing in separation and synthesis in catalysis science.