Supramolecular capsules can now be prepared with a wide range of volumes and geometries. Consequently, many of these capsules encapsulate guests selectively by size and shape, an important design feature for separations. To successfully address practical separations problems, however, a guest cannot simply be isolated from its environment; the molecular cargo must be removed to a separate physical space. Here we demonstrate that an (Fe4L4)-L-II coordination cage 1 can transport a cargo spontaneously and quantitatively from water across a phase boundary and into an ionic liquid layer. This process is triggered by an anion exchange from 1[SO4] to 1[BF4]. Upon undergoing a second anion exchange, from 1[BF4] to 1[SO4], the cage, together with its encapsulated guest, can then be manipulated back into a water layer. Furthermore, we demonstrate the selective phase transfer of cationic cages to separate a mixture of two cages and their respective cargoes. We envisage that supramolecular technologies based upon these concepts could ultimately be employed to carry out separations of industrially relevant compounds.