Chemical separations technologies are energetically costly; lowering this cost through the development of new molecular separation methods would thus enable significant energy savings. Molecules could, for example, be selectively encapsulated and separated using coordination cages, which can be designed with cavities of tailored sizes and geometries. Before cages can be used to perform industrially relevant separations, however, the experimental and theoretical foundations for this technology must be established. Using hydrophobic and hydrophilic anions as stimuli, we show that cages can reversibly transfer many times between mutually immiscible liquid phases, thus transporting their molecular cargoes over macroscopic distances. Furthermore, when two cages are dissolved together, sequential phase transfer of individual cage species results in the separation of their molecular cargoes. We present a thermodynamic model that describes the transfer profiles of these cages, both individually and in the presence of other cage species. This model provides a new analytical tool to quantify the hydrophobicity of cages.