Alzheimer first identified amyloid plaques during autopsies of the brains of dementia patients in 1905. Considerable effort has since been directed to understanding the composition, structure and formation mechanism of amyloid fibrils. A variety of proteins have now been shown to self-assemble into amyloid fibrils. Furthermore, the association between misfolded proteins and a wide range of diseases is now established. Here we examine the effect of shear on the formation, structure and mechanical properties of amyloid fibrils. Atomic force microscopy is used to both image and measure the nanomechanical properties of β-lactoglobulin (β-Lg) amyloid fibrils generated in controlled (Couette) and uncontrolled shear flows (stirring). Controlled shear-induced fibrils with ‘beaded’ morphologies have lower mechanical strengths than fibrils formed in uncontrolled shear which show twisted ribbon like morphologies. The mechanical strengths of amyloid fibrils are determined by fibril structure and vary depending on the type of shear exposure during in vitro formation. These findings may have implications regarding the different toxicities of amyloid fibrils and linear aggregates that form in vivo.