Atom probe microscopy (APM) is a relatively new in situ tool for measuring isotope fractions from nanoscale volumes (< 0.01 μm3). We calculate the theoretical detectable difference of an isotope ratio measurement result from APM using counting statistics of a hypothetical data set to be ± 4δ or 0.4% (2s). However, challenges associated with APM measurements (e.g., peak ranging, hydride formation and isobaric interferences), result in larger uncertainties if not properly accounted for. We evaluate these factors for Re‐Os isotope ratio measurements by comparing APM and negative thermal ionisation mass spectrometry (N‐TIMS) measurement results of pure Os, pure Re, and two synthetic Re‐Os‐bearing alloys from Schwander et al. (2015, Meteoritics and Planetary Science, 50, 893) [the original metal alloy (HSE) and alloys produced by heating HSE within silicate liquid (SYN)]. From this, we propose a current best practice for APM Re‐Os isotope ratio measurements. Using this refined approach, mean APM and N‐TIMS 187Os/189Os measurement results agree within 0.05% and 2s (pure Os), 0.6–2% and 2s (SYN) and 5–10% (HSE). The good agreement of N‐TIMS and APM 187Os/189Os measurements confirms that APM can extract robust isotope ratios. Therefore, this approach permits nanoscale isotope measurements of Os‐bearing alloys using the Re‐Os geochronometer that could not be measured by conventional measurement principles.