Diatoms are unicellular algae that are characterized by silica cell walls with intricate species-specific morphologies. Diatom silica is a sophisticated organic-inorganic hybrid material, hierarchically patterned with nano- and microscale pores, and serves as a spectacular example for the ability of biology to efficiently sculpt materials. The silica structures are formed intracellularly, in membrane-bound organelles named silica deposition vesicles (SDV). SDVs are delicate, elongated and flat (<200 nm) compartments that form a tightly confined and chemically regulated environment in which silica formation is strictly controlled. Due to limitations in conventional methods, the biological and chemical processes that control silica precipitation and morphogenesis are not completely understood. Here, we provide high-resolution 3D views of the SDV in the model diatom species Thalassiosira pseudonana. Diatom cells were preserved in their native state by plunge freezing, milled to thin lamellae using a focused ion beam, and imaged using cryo electron tomography. The 3D in situ data cover all stages of the silicification process, revealing the developmental sequence of the SDV and forming silica precipitates at nanometer resolution. Our data emphasize the close proximity between the plasma membrane and the SDV membrane, suggesting a functional interaction during silicification. Our work demonstrates the strength of cryo electron tomography to study the biological processes underlying biosilicification, as it elucidates the role of the SDV membrane in structure determination of the inorganic phase.