Xenotime (YPO₄) is an accessory phase common in low to high-temperature geological environments. Xenotime is an established geochronometer, though its small size, low modal abundance and textural complexity make it more difficult to analyse with traditional techniques but makes a prime candidate for nanoscale analysis. In this study, we develop an atom probe tomography (APT) protocol to determine the ²⁰⁶Pb/²³⁸U and ²⁰⁷Pb/²⁰⁶Pb ages of micro-scale xenotime crystals with analytical volumes four to six orders of magnitude smaller than typical geochronology techniques. A linear correlation between the ²⁰⁶Pb/²³⁸U fractionation and ²³⁸UO₂²⁺/²³⁸UO²⁺ was used to correct for the atom probe instrument parameters variability between specimens. For ²⁰⁷Pb/²⁰⁶Pb ages, we employed two methods of background correction owing to the ²⁰⁶Pb²⁺ thermal tail contribution to the ²⁰⁷Pb²⁺ counts: A constant background correction for the younger (~ 1000 Ma) Y1 reference material and a variable correction of background for Archaean age reference material xtc to correct for the thermal tail influence. This contribution also proposes strategies for optimisation of xenotime analysis using APT and permits us to explore the various geological problems in the nanoscale realm. This methodology potentially allows determining the age of small xenotime crystals in sedimentary rocks, low metamorphic grade settings and deformation microstructures.