Fluorescent nanoparticles with bright, narrowband emissions are highly sought after for applications in bio-labelling, quantum communications and sensing. Diamond nanocrystals are attracting major attention in this regard 1-9 due to their ability to host room temperature, photostable single photon emitters 10 . Several known optically active defects such as the nitrogen vacancy (NV) 11 and silicon vacancy (SiV) 12 have been studied extensively and their photophysical properties are well understood. Yet, diamond can host many other colour centres that have not been explored to date [13][14] and their origin remains unknown. While some of these centres can be engineered using ion implantation techniques 15 , this avenue is not ideal, due to the damage caused by ion bombardment 16 . It is therefore highly desirable to understand emitter formation mechanisms in damage-free, scalable, bottom-up techniques such as chemical vapour deposition (CVD). During CVD, a growing diamond crystal often incorporates silicon and other impurities 17 . This has been utilized extensively to engineer SiV 12 and other single photon emitters [18][19] in both individual nanodiamonds as well as polycrystalline films [20][21] . The process is, however, stochastic and improved control is needed over emitter concentrations and distributions. It is imperative to understand the underlying mechanisms and to achieve greater control over the incorporation of narrowband emitters in fluorescent nanodiamonds, which is essential for quantum photonic devices as well as bio-imaging applications.