Proteinous materials, such as soy protein isolate (SPI), have drawn tremendous attention as an economical biological resources for materials applications, due to their inarguably outstanding sustainability and promising properties and functionalities. To achieve precise materials design and fabrication, the knowledge of materials structure-property relationship is demanded. However, proteins are known for their complex structures consisting of about 20 different types of randomly and covalently bonded amino acids. The diverse inter-/intra-molecular interactions further complicate the aggregated protein structures in the solid state. Currently, the knowledge of solid-state protein structures and their relationship with properties of protein-based materials is inadequate, due to the limitation of modern characterization technologies. X-ray photoelectron spectroscopy (XPS) is a surface analysis technique that can measure the elemental and chemical state for less than 10 nm from the surface and can be quantified without a known standard, superior to many other technologies. Meanwhile, via analysis of the heterogenous elemental distributions, the aggregated protein structures, dominated by the peptide bonds, were revealed. The presence of dimethyl sulfide and glycerol in SPI significantly affected the elemental distribution but did not noticeably impact the aggregation of peptide bonds. The nearly identical distributions of metallic elements from the ash compositions in SPI, such as Na and Ca, suggested their favorable binding with peptide bonds, which were not affected by the materials fabrication and modifiers. This study proves the feasibility of XPS in characterizing the heterogeneity of soy protein materials via identifying and quantifying the distributions of chemical states in soy protein, leading to new knowledge about the aggregated solid structures in soy protein materials.