Elastin‐like polypeptides (ELPs) have been proposed as a simple model of intrinsically disordered proteins (IDPs) which can form membrane‐less organelles via liquid‐liquid phase separation (LLPS) in cellular milieu. Herein, fluorescently labeled ELP is studied in cytomimetic aqueous two‐phase system (ATPS). Droplet‐based protocells are obtained in a microfluidic system, allowing for confinement, temperature changes and statistical analysis. The spatial organization of ELP is observed in such binary ATPS macrocrowders. In addition, owing to switch of conformational states, dynamic formation and distribution of ELP‐rich droplets within the artificial cytoplasm is triggered by temperature. Three‐dimensional structured proteins are concurrently encapsulated along with ELP in synthetic cells and distinct partitioning properties of these proteins and ELP in binary polymeric phases are observed. This underpinning discovery demonstrates that the ability of ELP to coacervate with temperature can be maintained inside intracellular mimetic medium, and the preferential distribution of ELP in macromolecular crowding.