During dough mixing chemical, biochemical and physical transformations occur that allow dough formation to be characterized by common chemical and biochemical methods. Recently, spectrometric methods were used to characterize the dough mixing. The Mid-infrared (MIR) and the Near-infrared (NIR) spectroscopy allow information concerning chemical content and composition of food products to be obtained. The aim of this study is to apply FT-NIR and FT-MIR spectroscopy to monitor dough chemical changes, and to correlate those signals by the 2D Cross-Correlation (2D CORR) method. The 2D CORR was used to emphasize chemical assignment of the NIR band modifications (particularly for protein) during dough mixing. The 2D CORR analysis of the raw NIR and MIR spectra demonstrated that five NIR regions are highly correlated to protein vibrations. The 2D CORR analysis of the NIR and MIR spectra after second derivative demonstrated that the amide bands present high R2 for the NIR bands at (1189–1216), (1351–1474) and (1873) nm. A low R2 is obtained between the amide I and amide II bands and the (2026–2123) and (2280–2325) nm regions. The amide III band presents a slightly higher R2 for those NIR regions. The 2D CORR analysis of NIR and MIR spectra allow more specific NIR regions associated to chemical modifications of protein structure to be identified. The 2D CORR analysis of the second derivative spectra is more precise for the identification of the NIR regions implied in dough mixing compared to the 2D CORR analysis of raw NIR and MIR spectra