Advancement in microstructural geochronology using atom probe tomography (APT) depends on baseline measurements and interpretive approaches using geochronology reference materials. Here we present the first APT results for the well-characterized baddeleyite from the 2.060 Ga Phalaborwa intrusion and reference zircon BR266 (0.559 Ga) to explore the applicable run conditions, peak identifications, ranging, and detection sensitivity of trace elements and Pb. Six microtips of monocrystalline baddeleyite, as confirmed by tEBSD, were analyzed in both the annealed (300°C) and un-annealed states. The analyzed stoichiometry of the primary constituents (Zr, O, Hf) yields the correct concentrations but with uncertainty of several percent due to analyst-dependent ranging. The distribution of trace elements is homogeneous, even for the annealed samples. APT analysis was able to detect 5 of the 10 known trace elements above the background level. Zircon BR266 is mostly homogeneous, and the bulk APT analysis of these domains yields the correct 206Pb/238U, and 207Pb/206Pb ages with large uncertainties. Rare nanoclusters of Pb yield similar Pb isotopic ratios to the bulk, whereas signal from the surrounding matrix is too low (~12 ppm atomic) to yield meaningful results. The approaches described here for these two important minerals are a guide to future geoscience applications with APT.