The silica skeleton of the deep-sea sponge Euplectella aspergillum was recently shown to be structured over at least six levels of hierarchy with a clear mechanical functionality. In particular, the skeleton is built of laminated spicules that consist, of alternating layers of silica and organic material. In the present work, we investigated the micromechanical properties of the composite material in spicules of Euplectella aspergillum and the giant anchor spicule of Monorhaphis chuni. Organic layers were visualized by backscattered electron imaging in the environmental scanning electron microscope. Raman spectroscopic imaging showed that the organic layers are protein-rich and that there is an OH-enrichment in silica near the central organic filament of the spicule. Small-angle x-ray scattering revealed the presence of nanospheres with a diameter of only 2.8 nm as the basic units of silica. Nanoindentation showed a considerably reduced stiffness of the spicule silica compared to technical quartz glass with different degrees of hydration. Moreover, stiffness and hardness were shown to oscillate as a result of the laminate structure of the spicules. In summary, biogenic silica from deep-sea sponges has reduced stiffness but an architecture providing substantial toughening over that of technical glass, both by structuring at the nanometer and at the micrometer level.