Photoluminescent molecules are widely used for real-time monitoring of peptide aggregation. In this Article, we detail both experimental and computational modeling to elucidate the interaction between [Ru(bpy)2dppz]2+ and amyloid-β (Aβ1–40) aggregates. The transition from monomeric to fibrillar Aβ is of interest in the study of Alzheimer’s disease. Concentration-dependent experiments allowed the determination of a dissociation constant of 2.1 μM, while Job plots provided a binding stoichiometry of 2.6 Aβ monomers per [Ru(bpy)2dppz]2+. Our computational approach that combines molecular docking (both rigid and flexible) and all-atom molecular dynamics (MD) simulations predicts that the hydrophobic cleft between Val18 and Phe20 is a plausible binding site, which could also explain the increase in photoluminescence of [Ru(bpy)2dppz]2+ upon binding. This binding site is parallel to the fibril axis, in marked contrast to the binding site of these complexes in DNA (perpendicular to the DNA axis). Other binding sites may exist at the edges of the Aβ fibril, but they are actually of low abundance in an Aβ fibril several micrometers long. The assignment of the binding site was confirmed by binding studies in an Aβ fragment (Aβ25–35) that lacked the amino acids necessary to form the binding site. The agreement between the experimental and computational work is remarkable and provides a general model that can be used for studying the interaction of amyloid-binding molecules to Aβ.