Biopolymer composites based on pea starch-protein blends and pea flour are processed using extrusion at various levels of specific mechanical energy (SME). Their morphology was a continuous matrix phase of starch with embedded protein particles, as revealed by Confocal Laser Scanning Microscopy (CLSM). The motivation is to correlate the local Young's modulus (E) in starch and protein phases, as well as their interphase, through nanoindentation tests to macroscopic three-point bending testing results of starch-protein composites. The differences between E of starch and protein phases and interphase were significant and their values were found to vary in the ranges of 4.2–7, 3–6.9 and 4–6.9 GPa, respectively. The local E can be tuned by the protein content and composite morphology, the latter depending on the level of transformation of the biopolymers during extrusion (SME). Pea flour composites have larger modulus values, which can be attributed to the presence of fibres.