Here we report an NMR study on the substrate interaction modes of GroEL using amyloid β (Aβ) as a model ligand. We found that GroEL could suppress Aβ(1–40) amyloid formation by interacting with its two hydrophobic segments Leu17-Ala21 and Ala30-Val36, which involve key residues in fibril formation. The binding site of Aβ(1–40) was mapped on a pair of α-helices located in the GroEL apical domain. These results provide insights into chaperonin recognition of amyloidogenic proteins of pathological interest.