Wheat gluten (WG) and potato protein (PP) were modified to a basic pH by NaOH to impact macromolecular and structural properties. Films were processed by compression molding (at 130 and 150 °C) of WG, PP, their chemically modified versions (MWG, MPP) and of their blends in different ratios to study the impact of chemical modification on structure, processing and tensile properties. The modification changed the molecular and secondary structure of both protein powders, through unfolding and re-polymerization, resulting in less cross-linked proteins. The β-sheet formation due to NaOH modification increased for WG and decreased for PP. Processing resulted in cross-linking of the proteins, shown by a decrease in extractability; to a higher degree for WG than for PP, despite higher β-sheet content in PP. Compression molding of MPP resulted in an increase in protein cross-linking and improved maximum stress and extensibility as compared to PP at 130 °C. The highest degree of cross-linking with improved maximum stress and extensibility was found for WG/MPP blends compared to WG/PP and MWG/MPP at 130 °C. To conclude, chemical modification of PP changed the protein structures produced under harsh industrial conditions and made the protein more reactive and attractive for use in bio-based materials processing, no such positive gains were seen for WG.