Understanding bio-based protein polymer structures is important when designing new materials with desirable properties. Here the effect of urea on the wheat gluten (WG) protein structure in WG-urea films was investigated. Small-angle X-ray scattering indicated the formation of a hexagonal close-packed (HCP) hierarchical structure in the WG-urea materials. The HCP structure was influenced significantly by the urea concentration and processing conditions. The interdomain distance d I between the HCP scattering objects increased with increasing content of urea and the objects seemed to be oriented in the extrusion direction. Additionally, the effect of temperature on the HCP structure was studied and it was shown that at ≥55°C the HCP structure disappeared. Transmission electron microscopy revealed a rather denatured pattern of both HMW-glutenins and gliadins in the WG-urea films. The molecular packing of the WG protein polymer can be highly affected by an additive and the processing method used.