Biomineralizing organisms can grow nanomaterials with unexpected morphologies in an organic matrix where temporal and vectorial gradients of crystal growth precursors are established. Here, concentration gradients for the crystallization of gold nanoparticles are generated and applied on silicon substrates. Gradients of crystal growth precursors are generated by enzymes patterned as lines that are separated by distances ranging from the micro- to the nanoscale. The concentration of crystallization precursors around the lines separated by nanometric distances is not only determined by mass transport and enzyme activity but also by the nanoscale organization of biocatalysts. This nanoscale organization favors non-classical crystal growth conditions that lead to the formation of nanoparticle clusters containing nanocrystals that are highly crystallographically aligned. The combination of bottom-up crystal growth with top-down electron beam lithography enables the fabrication of micrometric patterns containing gold nanoparticles of different size, shape, and surface density. These are all critical parameters that determine the physical properties of these nanomaterials.