To ensure survival, the exoskeletons of biological species are required to minimize the spatial extent of damage following attack or multi-hit events. Now, nanoindentation experiments on a transparent bivalve shell, which is made up of layered, diamond-shaped calcite crystals, show an increased energy dissipation density compared with single-crystal calcite, resulting in penetration resistance and deformation localization. The detailed mechanisms of this enhanced energy dissipation are revealed and include nanoscale deformation twinning around the penetration zone.