Chemical purifications are critical processes across many industries, requiring 10 - 15% of humanity’s global energy budget1,2. Coordination cages are able to catch and release guest molecules based upon their size and shape3,4, providing a new technological basis for achieving chemical separation. Here we show that aqueous solutions of FeII4L6 and CoII4L4 cages can be used as liquid membranes. Selective transport of complex hydrocarbons across these membranes enabled the separation of target compounds from mixtures under ambient conditions. The kinetics of cage-mediated cargo transport are governed by guest binding affinity. Using sequential transport across two consecutive membranes, target compounds were isolated from a mixture in a size-selective fashion. The selectivities of both cages thus enabled a two-stage separation process to isolate a single compound from a mixture of physicochemically similar molecules.