The Middle-Late Permian Yakshawa bauxite deposit in the Sanandaj-Sirjan Zone and the Late Cretaceous Daresard bauxite deposit in the Zagros Fold-Thrust Belt have bauxite ores with different textures and mineralogical compositions. The presence of detrital and authigenic REY-phosphates, fluorocarbonates of the bastnasite group, and cerianite with diverse generations reflect an intricate formation process of the REY-bearing minerals in these two deposits. This clearly shows that the studied deposits have a multi-stage evolution including diagenetic and/or low-grade metamorphic, in situ fluid-assisted dissolution–reprecipitation reactions, and later bauxitization. The high abundance of monazite, textural relationships, and its LREE pattern indicate this mineral is the main LREE reservoir in the studied bauxite ores whereas xenotime, both authigenic and detrital, is the main host for HREE. The R-mode factor analyses indicates that the bauxitization process induces, at large, similar interelemental relationships in the studied deposits involving the attitude of Al oxyhydroxides, Ti oxides, and Fe oxyhydroxides to concentrate critical metals and the capability of REY-phosphate of being the main reservoir of REE + Y. As for provenance, the Eu/Eu*, Sm/Nd, and Nb/Ta proxies suggest that the bauxite ores of the Yakshawa deposit have a genetic relationship with Middle-Late Permian mafic volcanic rocks, whereas the ores of the Daresard deposit show parental affinity with the underlying fine-grained clayey limestone of the Sarvak Formation.