We report the molecular self-assembly of two amphiphilic peptides (A₆K and V₆K) and the application of their self-assemblies as organic templates to direct biosilica formation. Under ambient conditions, A₆K self-assembled into nanotubes 2.7 nm tall and approximately 1 μm to 2 μm long. In contrast, V₆K self-assembled into lamellar-stack nanostructures approximately 4 nm tall and under 100 nm long. The self-assembled peptide nanostructures were used as organic templates to direct biosilica formation. Comparing with the self-assembled structures formed by the peptide/anions system, novel silica morphologies can be obtained by changing the peptide composition, using different anions, and applying electrostatic/flow fields. We observed that the presence of anions is important but not enough to produce ordered silica structures with novel morphologies. This study provides further understanding of silica biomineralization tailored by assembled peptides, which offers a simple but efficient method to control the formation of inorganic material.