The transmissible spongiform encephalopathies are a family of diseases characterized by abnormal folding and aggregation of the prion protein. One of the directions in the search for cure for these and other amyloid diseases focuses on the inhibition of protein aggregation by small molecules, short peptides, and nanoparticles. Nanoparticles seem to be particularly promising therapeutic candidates since they are stable, can be made biocompatible, and might readily traverse physiological barriers such as the blood–brain barrier. Here, a novel class of chiral amyloid inhibitors consisting of carbon quantum dots (C-dots) that are synthesized from either d- or l-lysine (Lys) as the sole carbonaceous building block are reported. The interactions of the chiral lys-C-dots with the amyloidogenic determinant of the prion peptide (PrP, 106–126 sequence) in the presence of lipid bilayers appears to be highly stereoselective, with the l-Lys-C-dots being superior to the d-Lys-C-dots in their ability to modulate the structural transformations and aggregation of PrP(106–126). This work provides new insights into chiral effects upon amyloid peptides and opens the way to developing chiral carbon-based nanostructures as advanced amyloid inhibitors. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim