We report a method for creating synthetic diatom frustules via the biomimetic silicification of polyamine-rich scaffolds assembled by direct ink writing (DIW) [G. M. Gratson, M. Xu and J. A. Lewis, Nature, 2004, 428, 386, ]. A concentrated polyamine-rich ink is robotically deposited in a complex 3D pattern that mimics the shape of naturally occurring diatom frustules, Triceratium favus Ehrenberg (triangular-shaped) and Arachnoidiscus ehrenbergii (web-shaped). Upon exposing these scaffolds to silicic acid under ambient conditions, silica formation occurs in a shape-preserving fashion. Our method yields 3D inorganic–organic hybrids structures that may find potential application as templates for photonic materials, novel membranes, or catalyst supports.