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Diamond has established itself as an ideal material for photonics and optomechanics, due to its broad-band transparency and hardness. In addition, colour centres hosted within its lattice such as the nitrogen-vacancy (NV) centre, have become leading candidates for use in quantum information processing, and quantum sensors. The fabrication of nanoscale devices coupled to high quality NVs has been an outstanding challenge due to their sensitivity to magnetic, electric and strain fields within their local environment. In this work, we show how the NV centre’s ground state electron spin can be used as an embedded atomic-scale probe of the local strain caused by focused ion beam milling of nanoscale devices. This technique can thus be used to measure, and optimise material and device fabrication processes to allow diamond to reach its full potential.