<p>This study systematically investigated the leaching efficacy and mechanisms of La³⁺ and Y³⁺ from the clay minerals kaolinite and halloysite by <i>Aspergillus niger, Acidithiobacillus ferrooxidans</i>, and typical metabolites (citric acid and protease). The results indicated that nearly complete leaching of rare earth ions was achieved by <i>A. niger, A. ferrooxidans</i>, their fermentation broths, and citric acid. <i>A. niger</i> dissolves rare earth ions mainly by secreting organic acids, which form soluble complexes to promote mineral dissolution and increase ion-exchange release. In contrast, <i>A. ferrooxidans</i> oxidizes elemental sulfur to generate sulfuric acid, significantly reducing the system’s pH and enhancing the leaching process. However, both microorganisms adsorbed free rare earth ions during the later stages of leaching, leading to a decrease in their concentrations in the solution. Citric acid significantly improved the solubility of rare earth elements through complexation, whereas proteases showed relatively poor leaching efficiency for clay minerals. Phase composition and surface functional group analyses revealed notable changes in the O-H and C=O groups of kaolinite and halloysite after treatment with microbes and their metabolites, which increased mineral reactivity. This research provides a theoretical basis and technical support for the green and efficient recovery of rare earth resources from clay minerals.</p>