Silica-chitosan hybrid beads were synthesized via three different methods to investigate the selective recovery of REE from AMD. The influence of amino/non-amino silanes, high molecular weight/high viscous chitosan and N-/O- based ligands were studied and their effects on REE removal efficiencies were analyzed. The adsorption efficiencies of three various groups of modified beads were inspected with respect to feed pH, in a single and a multi-component system, and their affinities towards the light and heavy rare earth elements (LREE/ HREEs) were interpreted to understand the intra-series REE separation behavior. The focus of the study was mainly directed towards utilizing these fabricated beads for the recovery of valuable REEs from the real AMD obtained at three different sampling depths which was found rich in iron, sulfur and aluminum. Moreover, the selectivity of the beads towards REEs improved with silanized and ligand immobilized gels and their impacts on REE recovery in the presence of competing ions were successfully presented in this paper. Also, the synthesized beads showed rapid REE adsorption and recovery within a process time of 5 min. Group II adsorbents, synthesized by forming silica-chitosan hybrid beads followed by PAN/acac modifications, showed superiority over the other groups of adsorbents.