Through precise control of nanoscale building blocks, such as proteins and polyamines, silica condensing microorganisms are able to create intricate mineral structures displaying hierarchical features from nano- to millimeter-length scales. The creation of artificial structures of similar characteristics is facilitated through biomimetic approaches, for instance, by first creating a bioscaffold comprised of silica condensing moieties which, in turn, govern silica deposition into three-dimensional (3D) structures. In this work, we demonstrate a protein-directed approach to template silica into true arbitrary 3D architectures by employing cross-linked protein hydrogels to controllably direct silica condensation. Protein hydrogels are fabricated using multiphoton lithography, which enables user-defined control over template features in three dimensions. Silica deposition, under acidic conditions, proceeds throughout protein hydrogel templates via flocculation of silica nanoparticles by protein molecules, as indicated by dynamic light scattering (DLS) and time-dependent measurements of elastic modulus. Following silica deposition, the protein template can be removed using mild thermal processing yielding high surface area (625 m(2)/g) porous silica replicas that do not undergo significant volume change compared to the starting template. We demonstrate the capabilities of this approach to create bioinspired silica microstructures displaying hierarchical features over broad length scales and the infiltration/functionalization capabilities of the nanoporous silica matrix by laser printing a 3D gold image within a 3D silica matrix. This work provides a foundation to potentially understand and mimic biogenic silica condensation under the constraints of user-defined biotemplates and further should enable a wide range of complex inorganic architectures to be explored using silica transformational chemistries, for instance silica to silicon, as demonstrated herein.