Mapping the nanomechanical properties of amyloids can provide valuable insights into structure and assembly mechanisms of protein aggregates that underlie the development of various human diseases. Although it is well-known that amyloids exhibit an intrinsic stiffness comparable to that of silk (1–10 GPa), a detailed understanding of the directional dependence (anisotropy) of the stiffness of amyloids and how it relates to structural features in these protein aggregates is missing. Here we used steered molecular dynamics (SMD) simulations and amplitude modulation–frequency modulation (AM–FM) atomic force microscopy to measure the directional variation in stiffness of GNNQQNY amyloid crystals. We reveal that individual crystals display significant mechanical anisotropy and relate this anisotropy to subtle but mechanically important differences in interactions between interfaces that define the crystal architecture. Our results provide detailed insights into the structure–mechanics relationship of amyloid that may help in designing amyloid-based nanomaterials with tailored mechanical properties.