Molecular compartmentalization is a hallmark of living systems. Likewise, a molecular factory is envisaged to contain molecular modules/reactors that function within a membrane-bound environment. Importantly, the requisite modules have to be selectively imported into and/or compartmentalized within the molecular factory, whilst exporting the by-products. Here, our goal is to engineer nanoporous proteoliposomes that import, compartmentalize and accumulate specific macromolecular modules against concentration gradients. Such a “molecular logistics” system draws inspiration from living cells, where ~50 nm-diameter nuclear pore complexes (NPCs) regulate the selective transport of large cargoes (e.g. mRNA) in and out of the nucleus (Grünwald et al. Nature 2011).