The causes of U-Pb isotopic discordance documented by Paquette et al. (2004) in monazite grains from the ultra-high temperature (UHT) granulite of the Andriamena unit of Madagascar are reevaluated in the light of nanoscale crystal-chemical characterization utilising Atom Probe Tomography (APT) and state-of-the-art Scanning Transmission Electron Microscopy (STEM). APT provides isotopic ( 208 Pb/ 232 Th) dating and information on the chemical segregation of trace elements (e.g., Pb) in monazite at nanoscale. Latest generation of STEM allows complementary high-resolution chemical and structural characterization at nanoscale. In situ isotopic U-Pb dating with Secondary Ion Mass Spectrometry (SIMS) on 25 monazite grains and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) on zircon have been employed to refine the age spectra. Monazite and zircon grains located in quartz and garnet formed with the peak UHT metamorphic assemblage, which is partially overprinted by retrograde coronitic textures. Zircon grains hosted in garnet and in quartz yield concordant U-Pb ages at 2758 ± 28 Ma and 2609 ± 51 Ma, respectively whereas monazite grains hosted in quartz and garnet show a discordant Pb * loss trend on the Concordia diagram recording disturbance at 1053 ± 246 Ma that is not seen by the zircon, underlining the importance of combining the use of monazite and zircon to understand the history of polymetamorphic rocks. The Pb * -loss trend of monazite is related to petrographic position, with less Pb * lost from monazite hosted in quartz and garnet than monazite hosted in the coronitic reaction texture domains. STEM shows that the garnet-and quartz-hosted monazite grains contain more Pb-bearing nanophases than monazite grains located in the coronitic textures. An inverse correlation between the number of Pb-bearing nanophases and the percentage of Pb * -loss in monazite grains demonstrates that Pb * is retained in the grain in the form of nanophases. The formation of Pb-bearing nanophases limits Pb * -loss at the grain scale and therefore allows the preservation of early events. 208 Pb/ 232 Th ratios obtained with APT in monazite located in quartz and garnet and excluding Pb * -bearing nanophases indicate a mean age of 1059 ± 129 Ma corresponding to a disturbance event hitherto undetected in the geochronological record of the Andriamena unit. Thus, geochronology with APT allows access to information and the definition of events that may be blurred or obscured when examined at lower spatial resolution.