Understanding and mimicking the hierarchical structure of mineralized tissue is a challenge in the field of biomineralization and is important for the development of scaffolds to guide bone regeneration. Bone is a remarkable tissue with an organic matrix comprised of aligned collagen bundles embedded with nanometer-sized inorganic hydroxyapatite (HAP) crystals that exhibit orientation on the macroscale. Hybrid organic–inorganic structures mimic the composition of mineralized tissue for functional bone scaffolds, but the relationship between morphology of the organic matrix and orientation of mineral is poorly understood. Herein the mineralization of supramolecular peptide amphiphile templates, that are designed to vary in nanoscale morphology by altering the amino acid sequence, is reported. It is found that 1D cylindrical nanostructures direct the growth of oriented HAP crystals, while flatter nanostructures fail to guide the orientation found in biological systems. The geometric constraints associated with the morphology of the nanostructures may effectively control HAP nucleation and growth. Additionally, the mineralization of macroscopically aligned bundles of the nanoscale assemblies to create hierarchically ordered scaffolds is explored. Again, it is found that only aligned gel templates of cylindrical nanostructures lead to hierarchical control over hydroxyapatite orientation across multiple length scales as found in bone.