Wheat contributes 19% of protein in the global human diet. Mid-infrared spectroscopy (MIR) combined with attenuated total reflection (ATR) is an excellent analytical method for assessing the chemical composition of complex biological samples. In contrast to established techniques used for wheat protein analysis, we show that by using ATR-MIR the protein secondary structures of different fractions can be studied. We found that albumin and globulin fractions were primarily composed of α-helix, with proportions of 57.8% and 45.9%, respectively. Gliadins, meanwhile, contained 38.3% β-turn and 36.9% α-helix, while glutenins predominantly exhibited 44.8% β-turn secondary structures. In addition, we found that by using analysis of variance (ANOVA) simultaneous component analysis (ASCA), the obtained MIR spectra of the wheat protein fractions were significantly (p < 0.001) affected by the sampling sites and variety. Quantification of the protein content of each sample through the amide II band also revealed significant differences (p < 0.001) across the sampling sites in the different protein fractions. The found concentration range of protein fractions within the wheat samples were as follows: 1.7-3.6, 0.4-2.4, 4.0-5.4, and 0.8-4.8 g/100 g of albumins, globulins, gliadins, and glutenins, respectively. In conclusion, this study shows that ATR-MIR has an immense potential for wheat proteome analysis.