Polymeric systems that self-assemble through strong noncovalent bonds form structures that are highly dependent on the spatiotemporal sequence of cues that trigger self-assembly. Here, we prepared capsules with a semipermeable alginate–chitosan polyelectrolyte membrane that encapsulates a solution of the pH-responsive self-assembling aminopolysaccharide chitosan. Immersion of these capsules in a basic solution triggers gelation of the capsule contents, and the details of the gel-inducing treatment dramatically affect the final structure of the gelled compartment. Specifically, we show that the sequential transfer of the capsules between the base and water can generate multilayer hydrogel structures, with the thickness of each layer being controlled by the base concentration and immersion times. We further demonstrate that these multilayer hydrogels can serve as templates for the synthesis of iron oxide particles with a complex internal structure (i.e., with a multilayer internal structure). This work demonstrates the ability to enlist the stimulus-responsive self-assembling properties of biological polymers to create materials with complex structures.