High volume production of plastic parts typically requires a short cycle time to drive the economics in a favorable direction. Reducing the cycle time during injection molding requires not only good understanding of the processing conditions but also how the material behaves in the melt and during cooling. On the other hand, processing history could also influence the mechanical properties. In this study, the thermal and mechanical properties of Novatein, a protein-based thermoplastic, was studied using synchrotron-based X-ray scattering and infrared spectroscopy. The high intensity of the light source makes it possible to take X-ray measurements at short time intervals during mechanical loading, while under infrared light, the conformation of the protein chains can be spatially resolved. It was found that the most prevailing chain structure is random coils, but, Novatein is highly aggregated into beta-sheets that are uniformly distributed in the sample along with a lesser amount of alpha-helices. These structures do not melt during processing and despite the semi-crystalline nature the material behaves more like a filled amorphous material during processing. Wide angle X-ray scattering revealed significant alignment of these chain structures under tension as a result of the deformation that occurs during loading. The additives used to produce Novatein influences the rate at which these changes occur and ultimately dictates cycle time during injection molding as well as mechanical properties.