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Abstract Solid-state spin qubits within silicon crystals at mK temperatures show great promise in the realisation of a fully scalable quantum computation platform. Qubit coherence times are limited in natural silicon owing to coupling to the 29Si isotope which has a non-zero nuclear spin. This work presents a method for the depletion of 29Si in localised volumes of natural silicon wafers by irradiation using a 45 keV 28Si focused ion beam with fluences above 1 × 1019 ions cm−2. Nanoscale secondary ion mass spectrometry analysis of the irradiated volumes shows residual 29Si concentration down to 2.3 ± 0.7 ppm and with residual C and O comparable to the background concentration in the unimplanted wafer. After annealing, transmission electron microscopy lattice images confirm the solid phase epitaxial re-crystallization of the as-implanted amorphous enriched volume extending over 200 nm in depth.