Amylin amyloid deposition is a common feature in the pancreas of type-2 diabetic (T2D) patients, and may play a role in islet beta-cell death and disease development. Type-2 diabetes is also characterised by a dysregulation of systemic copper. While the relationship between these features is unclear, previous work has shown that copper can form a complex with amylin, which in turn prevents amylin misfolding, oligomerisation and fibril formation, and that this in turn decreases amylin-mediated cytotoxicity. To date, the nature of this interaction has not been determined. In this study, we have used ion mobility mass spectrometry to probe the effects of copper on amylin oligomer formation and to define the binding site(s) of copper on the amylin peptide. Here we show that there are two distinct sites to which copper can bind. The first is at a location in the C-terminal 5 amino acids of the peptide. The second is on Ala25, a residue which is known to be critical for the misfolding ability of human amylin. This interaction is not observed under standard mass spectrometry (acidic) conditions but is present at physiological pH values. These data further characterise the amylin–copper interaction, and may suggest a potential trigger for amylin misfolding in T2D.