Soy protein-based blends were processed by double screw extrusion and the effects of different types and contents of polysaccharides were analyzed. Although extrusion has not been widely used for this type of blends, in this study it was observed that the increase in polysaccharide content in blends caused a decrease in specific mechanical energy (SME), facilitating extrusion process and showing the potential of this process, which is more cost effective at industrial scale. In order to explain this behavior, infrared spectroscopy analysis was carried out, mainly in the amide I and II regions. Moreover, curve fitting analysis showed the conformational changes produced in the blends due to the addition of polysaccharides, which affected protein denaturation. These changes also affected properties such as moisture content (MC) and total solubility matter (TSM). However, conformational changes did not show significant effects with respect to piece density (PD) or in the expansion ratio (ER) of the pellets. The quantitative analysis of the changes in the amide I and II regions provided novel information about the modifications produced in protein-based blends modified with polysaccharides. In this context, infrared spectroscopy provided a convenient and powerful means to monitor interactions between all ingredients used in the blend formulation, which is of great importance in order to explain changes in the functional properties of biodegradable materials used for industrial applications in food and pharmaceutical industries.