Natural nanoparticles are fundamental building blocks of Earth's bio- and geosphere. Amorphous silica nanoparticles are ubiquitous in nature, but fundamental knowledge of their interaction mechanisms and role in mineral replacement reactions is limited. Here we show how silica nanoparticles replace Cretaceous calcite bivalve shells in a volume- and texture-preserving process. Electron tomography reveals that mineral replacement transfers calcite crystallographic orientations to twinned photonic crystals composed of face-centered cubic silica sphere stacks. During the face-specific replacement process, silica nanoparticles continuously nucleate, aggregate, and form a lattice of uniform spheres parallel to calcite low-energy facets. We explain the replacement process with a new model that unifies recently proposed, probably universal mechanisms of interface-coupled dissolution-precipitation and aggregation-based crystallization; both key mechanisms in geological processes and nanomaterials design and synthesis.