Silicon is an attractive material for anodes in energy storage devices, because it has ten times the theoretical capacity of its state-of-the-art carbonaceous counterpart. Silicon anodes can be used both in traditional lithium-ion batteries and in more recent Li-O2 and Li-S batteries as a replacement for the dendrite-forming lithium metal anodes. The main challenges associated with silicon anodes are structural degradation and instability of the solid-electrolyte interphase caused by the large volume change (∼300%) during cycling, the occurrence of side reactions with the electrolyte, and the low volumetric capacity when the material size is reduced to a nanometre scale. Here, we propose a hierarchical structured silicon anode that tackles all three of these problems. Our design is inspired by the structure of a pomegranate, where single silicon nanoparticles are encapsulated by a conductive carbon layer that leaves enough room for expansion and contraction following lithiation and delithiation. An ensemble of these hybrid nanoparticles is then encapsulated by a thicker carbon layer in micrometre-size pouches to act as an electrolyte barrier. As a result of this hierarchical arrangement, the solid-electrolyte interphase remains stable and spatially confined, resulting in superior cyclability (97% capacity retention after 1,000 cycles). In addition, the microstructures lower the electrode-electrolyte contact area, resulting in high Coulombic efficiency (99.87%) and volumetric capacity (1,270 mAh cm(-3)), and the cycling remains stable even when the areal capacity is increased to the level of commercial lithium-ion batteries (3.7 mAh cm(-2)).