Control over the quantum states of individual luminescent nitrogen‐vacancy (NV) centres in nanodiamonds (NDs) is demonstrated by careful design of the crystal host: its size, surface functional groups, and interfacing substrate. By progressive etching of the ND host, the NV centres are induced to switch from latent, through continuous, to intermittent or “blinking” emission states. The blinking mechanism of the NV centre in NDs is elucidated and a qualitative model proposed to explain this phenomenon in terms of the centre electron(s) tunnelling to acceptor site(s). These measurements suggest that the substrate material and its proximity to the NV are responsible for the fluorescence intermittency.