Clay-hosted Rare Earth Element (REE) deposits are increasingly recognised as a potentially important future source of REEs. However, their fine-grained clay-rich nature, and generally poorly understood mineralogy and deportment present significant challenges for conventional processing routes. The Jupiter clay-hosted REE deposit, located 60 km west of Mt. Magnet, Western Australia is currently Australia’s largest clay-hosted REE deposit with an Inferred Resource of 1.8 billion tonnes (Bt) at 1700 ppm Total Rare Earth Oxides (TREO*) at a 1000 ppm lower cut-off. Extensive quantitative microanalysis (TIMA, LA-ICPMS and EPMA) conducted on the various mineralised materials, shows the REEs are largely deported to hydrated secondary REE phosphate phases including gorceixite-goyazite-florencite, rhabdophane-monazite and churchite-xenotime, within a matrix dominated by kaolinite, quartz, iron (hydr)oxides, minor titanium oxides, manganese (hydr)oxides, baryte, smectite, montmorillonite and vermiculite, and relict silicate and oxide phases. Both REE and gangue mineralogy is both vertically and laterally zoned reflecting an interplay between protolith composition and weathering intensity. (* TREO is the sum of La2O3, CeO2, Pr6O11, Nd2O3, Sm2O3, Eu2O3, Gd2O3, Tb4O7, Dy2O3, Ho2O3, Er2O3, Tm2O3, Yb2O3, Lu2O3, and Y2O3). The microanalytical work and mineralogical understanding led to a beneficiation first strategy to upgrade the REE phosphate mineral concentration and reduce gangue feed to conventional REE extractive processes. Beneficiation currently involves scrubbing attrition and targeted comminution followed by magnetic separation and flotation to selectively concentrate the key-REE bearing phosphate minerals. The initial REE mineral beneficiation test work demonstrated a 6–10 times REE upgrade with up to 96 per cent mass rejection to produce intermediate concentrates grading 1 2 per cent TREO at recoveries of 60–70 per cent of TREO from feed (in situ) grades of 1300 2200 ppm TREO. Further work continues improve REE concentrate grade and recovery. The results highlight the critical role of microanalytical techniques and mineralogical understanding in designing effective beneficiation strategies and demonstrate the potential of beneficiation-first flow sheets to improve the economic viability of clay-hosted REE deposits.