© 2016 Author(s). We demonstrate a self-aligned lithographic technique for precision generation of nitrogen vacancy (NV) centers within photonic nanostructures on bulk diamond substrates. The process relies on a lithographic mask with nanoscale implantation apertures for NV creation, together with larger features for producing waveguides and photonic nanocavities. This mask allows targeted nitrogen ion implantation, and precision dry etching of nanostructures on bulk diamond. We demonstrate high-yield generation of single NVs at pre-determined nanoscale target regions on suspended diamond waveguides. We report implantation into the mode maximum of diamond photonic crystal nanocavities with a single-NV per cavity yield of ∼26% and Purcell induced intensity enhancement of the zero-phonon line. The generation of NV centers aligned with diamond photonic structures marks an important tool for scalable production of optically coupled spin memories.