Granular protein is an important structural feature in determining starch digestibility. High-amylose wheat starch (HAWS) with >80% amylose content contains more granular protein than wild-type starch. As analyzed by mass spectrometry-based proteomics, granular-bound starch synthase (GBSS) is the major granular protein in isolated starch materials. GBSS content increases with amylose content (Spearman’s correlation, p < 0.05), whereas the abundance relative to other proteins is similar among starches. Multiple amylase inhibitors were also identified. From Michaelis–Menten analysis, HAWS has a similar Km (Michaelis constant) as wild type, suggesting initial enzymatic binding is similar. After the pre-digestion of proteins, wild type had a greater change in starch digestibility than HAWS, probably due to the latter having ‘thicker’ granular-protein layers and higher enzymatic resistance of substrate per se. Overall, the study suggests that the greater granular protein content in HAWS is a factor that contributes to slower amylolysis compared to wild type.