Coordination cages and their encapsulated cargo can be manoeuvred between immiscible liquid layers in a process referred to as phase transfer. Among the stimuli reported to drive phase transfer, counterion exchange is the most widespread. This method exploits the principle that counterions contribute strongly to the solubility preferences of coordination cages, and involves exchanging hydrophilic and hydrophobic counterions. Nevertheless, phase transfer of anionic cages remains relatively unexplored, as does selective phase transfer of individual cages from mixtures. Here we compare the phase transfer behaviour of two FeII4L6 cages with the same size and geometry, but with opposite charges. As such, this study presents a rare example wherein an anionic cage undergoes phase transfer upon countercation exchange. We then combine these two cages, and demonstrate that their quantitative separation can be achieved by inducing selective phase transfer of either cage. These results represent unprecedented control over the movement of coordination cages between different physical compartments, and are anticipated to inform the development of next-generation supramolecular systems.