Novatein thermoplastic protein embrittles quickly after processing due to desorption of plasticizer, leading to poor energy absorbing properties such as impact strength. However, impact modified Novatein blends, containing functionalized polyethylene or nano-scale core-shell particles exhibit increased energy absorbing properties. The phase distribution of reinforced blends, and the protein secondary structure changes as a result of blending and fracture was investigated using synchrotron FT-IR microspectroscopy. Morphological changes in Novatein/polyethylene blends were responsible for variations in mechanical properties, rather than changes in secondary structure. In contrast, a greater impact strength was correlated to an increase of disordered secondary structures in core-shell particle reinforced Novatein. Blends which exhibited greater elongation or yielding during fracture showed a significant difference between protein secondary structure in the bulk matrix and the yielded material after fracture. It was concluded that the change in conformation of protein structures during fracture is an energy absorbing mechanism that acts in conjunction with the free elongation of the matrix due to decreasing interparticle distance for materials reinforced with nano-particles. POLYM. ENG. SCI., 58:E124-E134, 2018. (c) 2017 Society of Plastics Engineers