Rare earth metals (REEs) are crucial for modern industries and technological development. Their extraction from non-renewable primary sources has almost reached its threshold due to excessive global demand. An effectual approach for REEs recovery is recycling secondary sources governed by separation materials. In this work, a novel glutenin-based Na-bentonite (Gle@Na_Bex:y) composite was produced via the in-situ hydrothermal route followed by a subsequent freeze-drying process. Additionally, a possible production route for the composites was proposed. The novel Gle@Na_Bex:y composites were characterized with Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), thermogravimetric analysis (TGA), Brunauer–Emmett–Teller (BET) surface area, and zeta potential (ZP) measurements. FTIR results complemented with SEM images and XRD measurements confirmed the successful incorporation of glutenin into the Na-bentonite clay. The separation of REEs from aqueous solution was used as a model system to demonstrate the material’s ability for selective metal recovery. The best conditions (T, pH, time) for REE sorption were assessed using equilibrium batch adsorption experiments. The kinetics of REE adsorption were effectively explained by a pseudo-second-order model; all the adsorption equilibrium data followed the Langmuir model. Thermodynamic investigations revealed that the adsorption is endothermic and spontaneous, and the adsorption of REEs occurred through a chemisorption process. The sorption mechanism of REE ions was investigated using molecular modelling. The results of this study demonstrate the feasibility of utilizing Gle@Na_Be50:50 composite as an efficient material for REEs removal. The maximum adsorption capacities of Y³⁺, La³⁺, and Nd³⁺ achieved with Gle@Na_Be_50:50, were 76.87, 56.71, and 74.61 mg/g, respectively. This work offers a new route for engineering, valuable composite materials for the separation of REEs from diverse sources.