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The Ambohimirahavavy igneous complex (Ampasibitika intrusion) in Madagascar hosts a world-class rare-earth element (REE) bearing ion-adsorption clay (IAC) resource. In this study, we present an in-depth chemical and mineralogical characterisation of selected samples from two regolith profiles at Ambohimirahavavy with a focus on REE geochemistry, mineralogy and associations with clay mineralogy. μ-Synchrotron X-ray fluorescence mapping was combined with traditional characterisation techniques in order to ascertain REE distribution within varying clay mineralogy. The ion-adsorption clays consist of aluminosilicate clay minerals (e.g. kaolinite, illite, smectite) formed through in-situ lateritic weathering of REE-rich host rocks. The new data reveal a high level of inhomogeneity in the samples at micro- to macroscopic levels. The ores are characterised by negative cerium anomalies, which are similar to those reported from the South China IAC ores, but contrast with positive anomalies reported in many regolith profiles developing on acid rocks, including in Madagascar. Ce-L III edge XANES spectroscopy shows that despite the negative Ce anomaly in the pedolith, Ce exists in trivalent form (mostly associated with clay minerals) and as Ce(IV); the latter is at least partially associated with textures reminiscent of the rhizosphere and with Mn- (and Fe-) oxides, highlighting the importance of micro-environments for Ce oxidation. The μSXRF images also reveal that a significant portion of REEs is associated with Zr; SEM imaging does not show the presence of Zr or REE (nano)-minerals, and the association is likely to reflect the decomposition of REE-Zr-rich host minerals and differential sorption of Zr and REEs on clay minerals. The Ambohimirahavavy ores are LREE-enriched, but contain HREE concentrations that are similar to those of the South China ores, making them an economically viable REE source. REE concentrations in the two studied profiles were particularly high in the saprolith relative to the pedolith, further contrasting with the South China ores, and indicating different mechanisms of ore formation. • Characterisation of a REE-rich ion-adsorption clay deposit in Madagascar • Significant differences in REE behaviour compared to South China ores • Samples with deep negative Ce anomalies still contain a significant amount of Ce(IV). • Zirconium-REE association at micron-level in ion-adsorption clay deposits [ABSTRACT FROM AUTHOR]