The synthesis of three-dimensional (3-D) assemblies of zirconia nanocrystals via the shape-preserving reactive conversion of biologically reproducible, silica-based microtemplates (diatom microshells) is demonstrated for the first time. Silica diatom microshells were first converted into magnesia replicas via an oxidation-reduction displacement reaction with magnesium gas. The magnesia replicas were then converted into zirconia replicas via a metathetic displacement reaction with zirconium tetrachloride gas. By utilizing both types of shape-preserving displacement reactions, bioclastic silica microtemplates may be converted into functional nanocrystalline assemblies with a variety of complex, but well-controlled 3-D shapes and chemistries for catalytic/chemical, biological, electrical, thermal, mechanical, and other applications.