The presence of an early Earth geodynamo has fundamental implications for planetary evolution and habitability for early life. Magnetite inclusions within ancient detrital zircon grains have the potential to record Earth’s magnetic field and provide a record of a geodynamo prior to 4 Ga. However, the interpretation of the magnetic signal within Jack Hills zircon has sparked intense debate. Some argue that it represents the primary magnetic field at the time of zircon crystallization, while others propose it represents a secondary magnetic overprint. A key aspect in both of these arguments is the timing of magnetite formation and the mobility of Fe within the zircon host; a constraint that has remained elusive using traditional geochronological techniques.  Here we undertake an investigation of highly magnetic zones of carefully selected ~4.0 Ga Jack Hills zircon using the nanoscale characterization capabilities of transmission electron microscopy (TEM) and atom probe tomography (APT). Microstructural analysis of the selected Jack Hills zircon grain reveals that magnetite inclusions are of secondary origin and are linked to the mobility of Fe. APT data uncovers the presence of Pb-bearing nanoclusters (~10 nm in diameter) that record elemental and isotopic compositions consistent with formation during two discrete thermal events at 3.4 Ga and < 2 Ga. The older population of clusters contain no detectable Fe, while the younger population contains Fe. These findings indicate that the Fe required to form secondary magnetite was not present in the zircon prior to 3.4 Ga. Furthermore, the remobilization of Pb and Fe, the latter associated with magnetite formation, took place after 2 Ga, more than one billion years after deposition of the Jack Hills sediment at 3 Ga. Our results demonstrate the innovative use of APT to yield direct age constraints on Fe mobility, ultimately verifying the Proterozoic age of the paleomagnetic signal recorded by ancient detrital Jack Hills zircon grains.