The design of compartmentalized carriers for advanced drug delivery systems or artificial cells and organelles is of interest for biomedical applications. Herein, a polymer carrier microreactor that contains two different classes of subcompartments, multilayered polymer capsules and liposomes, is presented. 50 nm-diameter liposomes and 300 nm-diameter polymer capsules are encapsulated into a larger polymer carrier capsule, demonstrating control over the spatial positioning of the subcompartments, which are either ‘membrane-associated’ or 'free-floating’ in the aqueous interior. Selective and spatially dependent degradation of the 300 nm-diameter subcompartments (without destroying the structural integrity of the enzyme-loaded liposomes) is also shown, by performing an encapsulated enzymatic reaction using the liposomal subcompartments. These findings cover several important aspects toward the development of engineered compartmentalized carrier vessels for the creation of artificial cell mimics or advanced therapeutic delivery systems.