The use of the abrasive milling allows to obtain flours with different composition; while, infrared spectroscopy was used in order to determine the change in the secondary structures of the proteins, and how this change affected the rheology of the flours. The spectra acquired at different milling time, presented the same bands of the transmittance observed in the whole flour. However, the transmittance ratio of 1545 cm−1/1022 cm−1 showed a significant increase compared to the whole flour. On the other hand, the transmittance ratio of 1653 cm−1/1022 cm−1 turned out to be less sensitive for the follow-up of the operation. Spectrum of the flour (FP10) showed greater intensity between the bands at 1620 cm−1 and 1640 cm−1, assigned to the β-sheet structures; while the bands at 1660 cm−1 and 1670 cm−1 (β-turns) showed less intensity. These differences were reduced with the increase in milling time. The pasting properties and water absorption index showed significant differences in most of the flours. These differences could be explained by the change in the secondary structures of the proteins, and the effect of the interaction of these with the starch in the heating and cooling process of the dispersions.