The geochemical analysis of trace elements in rutile (e.g., Pb, U, and Zr) is routinely used to extract information on the nature and timing of geological events. However, the mobility of trace elements can affect age and temperature determinations, with the controlling mechanisms for mobility still debated. To further this debate, we use laser-ablation–inductively coupled plasma–mass spectrometry and atom probe tomography to characterize the micro- to nanoscale distribution of trace elements in rutile sourced from the Capricorn orogen, Western Australia. At the >20 µm scale, there is no significant trace-element variation in single grains, and a concordant U-Pb crystallization age of 1872 ± 6 Ma (2σ) shows no evidence of isotopic disturbance. At the nanoscale, clusters as much as 20 nm in size and enriched in trace elements (Al, Cr, Pb, and V) are observed. The 207Pb/206Pb ratio of 0.176 ± 0.040 (2σ) obtained from clusters indicates that they formed after crystallization, potentially during regional metamorphism. We interpret the clusters to have formed by the entrapment of mobile trace elements in transient sites of radiation damage during upper amphibolite facies metamorphism. The entrapment would affect the activation energy for volume diffusion of elements present in the cluster. The low number and density of clusters provides constraints on the time over which clusters formed, indicating that peak metamorphic temperatures are short-lived, <10 m.y. events. Our results indicate that the use of trace elements to estimate volume diffusion in rutile is more complex than assuming a homogeneous medium.