Biopolymer composites made from blends of pea starch and protein, as well as pea flour, are produced using extrusion at different levels of specific mechanical energy (SME). Confocal Laser Scanning Microscopy (CLSM) shows that the composites have a continuous starch matrix containing dispersed protein particles. The goal of the study is to link the local Young's modulus (E) of the starch, protein, and their interphase—measured through nanoindentation tests—with the overall stiffness determined from three-point bending tests on the starch-protein composites. There were notable differences in the E values of the starch, protein, and interphase, ranging from 4.2 to 7 GPa, 3 to 6.9 GPa, and 4 to 6.9 GPa, respectively. The local E can be adjusted by altering the protein content and composite structure, which is influenced by the extent of biopolymer transformation during extrusion (SME). Composites made with pea flour exhibit higher modulus values, likely due to the presence of fibers.