Milled nanodiamonds containing nitrogen-vacancy (NV) centers provide an excellent platform for sensing applications as they are optically robust and have nanoscale quantum sensitivity. We developed a scalable strategy to form ordered arrays of nanodiamonds using capillary-driven, template-assisted self-assembly. By precisely placing 50 nm nanodiamonds across millimeter-scale areas we can study how variations in nanodiamond size, shape, and surface chemistry impact the particles’ optical and quantum characteristics. We have developed a tool for both fabricating new quantum devices and providing a deeper understanding of the material properties of nanodiamonds.