The significance of aggregated protein structures in tuning structures and dielectric polarization of poly(ethylene oxide) (PEO)/soy protein isolate (SPI) films was studied. The aggregated protein structures, subjected to denaturation processes, are expected to alter polymer-protein interactions, leading to diverse material structures, and properties. However, this is still insufficiently understood. In this study, SPI was modified via different denaturation processes including heat, sonication, and pH-control. According to structural analysis with scanning electron microscope, fluorescence imaging, X-ray diffraction, and Fourier transformed infrared spectroscopy, both denaturation conditions and SPI content affected PEO-SPI interactions, producing distinctive microstructures of PEO and SPI phases, which subsequently caused different dielectric properties in ferroelectric analysis. Particularly, sonication treated-SPI distinguished itself by generating a unique parabolic-like composition dependence of dielectric polarization, in contrast to other modified SPIs. Polymer/protein blends have shown great potential in biomedical and electronic applications, which will be further benefited by the findings in this study.