Microscale zirconia structures with intricate three-dimensional (3D) shapes and nanoscale features were synthesized using diatom (single-celled algae) microshells as transient scaffolds. After exposure to a zirconium alkoxide-bearing solution and firing at 550–850 °C, silica-based diatom microshells were coated with a thin, continuous nanocrystalline zirconia layer. Predominantly tetragonal or monoclinic zirconia could be produced with appropriate heat treatments. Selective silica dissolution then yielded freestanding zirconia micro-assemblies that retained the microshell shape and fine features. Such hybrid (biological/synthetic chemical) processing may be used to mass-produce nanostructured micro-assemblies with a variety of 3D, biologically replicable shapes and tailored compositions for use in numerous applications.