Rare earth elements (REYs) originate from the weathering of parent granite, whose clay-sized fractions are pivotal in the regolith-hosted rare earth elements (REEs) deposits. Regarding microbial action on REY mobilization and fractionation, their patterns remain unclear. Chemical extraction and bio-leaching experiments utilizing sulfate-reducing bacteria (SRB) were performed to exemplify the chemical and microbial effects on REY mobilization among the clay-sized phases. Our results indicate that the REYs occur primarily in the three fractions: i.e., amorphous FeMn phase, crystalline Fe phase, and carbonate in chemical reactors wherein the mineral phase was critical to the adsorption of REY. The 30-day SRB-leaching experiments led to an increase in the percentage of REY from 6% to 45% in the residue phase, implying that the residue phase, RAmor iron phase, and ROrg phase hosted the REYs. The disorder of iron-bearing minerals, formation of iron-organic matters (Fe-OM), and secondary iron-bearing minerals represented a significant bio-leaching mechanism. Compared to chemical extraction, relatively higher MREY and HREY release efficiencies were obtained via bio-leaching, with average LREY/HREY ratios of 1.34–5.91 and 0.2–2.24 in chemical and bio-reactors, respectively. Our findings exhibited high potential microbial effects on the mobilization and fractionation of REY among mineral phases, offering real insights into the biogeochemical processes between minerals and bacteria.