Complex structured soft matter may have important applications in the field of tissue engineering and biomedicine. However, the discovery of facile methods to exquisitely manipulate the structure of soft matter remains a challenge. In this report, a multilayer hydrogel is fabricated from the stimuli-responsive aminopolysaccharide chitosan by using spatially localized and temporally controlled sequences of electrical signals. By programming the imposed cathodic input signals, chitosan hydrogels with varying layer number and thickness can be fabricated. The inputs of electrical signals induce the formation of hydrogel layers while short interruptions create interfaces between each layer. The thickness of each layer is controlled by the charge transfer (Q = ∫idt) during the individual deposition step and the number of multilayers is controlled by the number of interruptions. Scanning electron micrographs (SEMs) reveal organized fibrous structures within each layer that are demarcated by compact orthogonal interlayer structures. This work demonstrates for the first time that an imposed sequence of electrical inputs can trigger the self-assembly of multilayered hydrogels and thus suggests the broader potential for creating an electrical "code" to generate complex structures in soft matter.