The spontaneous formation of patterns by multi-protein systems is essential for orchestrating fundamental biological processes like cell division and embryogenesis. Although various membrane proteins can generate patterns on continuous substrates, the mechanisms governing their self-organization on discontinuous, dispersed, and motile membranes, typical of intracellular environments, remain elusive. Here, we demonstrate that MinDE proteins, a prototypical pattern-forming system from E. coli, can form robust 3D patterns when interacting with a suspension of nanoscale liposomes, rather than a continuous 2D lipid membrane.