<p>Diabetes mellitus is a metabolic disorder that impacts millions of individuals globally. In the treatment of this condition, it is imperative to explore natural resources for therapeutic agents that exhibit fewer adverse effects and enhanced efficacy. Currently, the methods employed for isolating anti-diabetic lead compounds from natural sources are often intricate and time-consuming. Therefore, there is an urgent need to develop efficient and rapid screening techniques. In this study, α-amylase was immobilized using a novel polydopamine/L-cysteine bifunctionalized magnetic mesoporous silica composite material (Fe₃O₄@nSiO₂@mSiO₂@PDA@L-Cys) for the first time. A ligand fishing approach utilizing the immobilized α-amylase was developed to rapidly screen for α-amylase inhibitors from <i>Aloe vera</i>. Characterization and property analysis of the immobilized enzyme showed that the immobilized α-amylase exhibited exceptional stability and reusability. Two ligands were successfully screened from <i>Aloe vera</i> and then characterized as aloin B and aloin A using ultra-high performance liquid chromatography tandem mass spectrometry. Their respective IC₅₀ values were 0.99 ± 0.09&#xa0;mM and 1.14 ± 0.05&#xa0;mM. Molecular docking studies confirmed the interaction of both ligands with specific amino acid residues within the active site of α-amylase. The study presents a fast and efficient approach for screening α-amylase inhibitors from intricate natural sources, thereby offering significant potential for the development of anti-diabetic agents.</p> Graphical Abstract <p></p>