The effects of aging from t = 0–108 h at two different temperatures (4 and 25 °C) on the non-linear viscoelastic rheological properties and secondary protein structure of hard wheat flour dough (HWD) were investigated using large amplitude oscillatory shear tests (LAOS) coupled with Fourier transform infrared spectroscopy (FTIR) and SDS-PAGE. Storage (G') and loss (G'') moduli rapidly decreased during aging at 25 °C. Subjecting HWD to progressively longer aging times at 25 °C caused dramatic changes in the non-linear viscoelastic properties demonstrated by strain softening (negative values of e3/e1) and shear thinning (negative values of v3/v1) behavior. Elastic Lissajous curves of the unaged control dough showed clockwise turn and wider elliptical trajectories as dough aging proceeds especially at higher temperatures. Other non-linear LAOS parameters (G'M-G''L, η'M-η'L, S and T) supported that aging process at higher temperature caused a progressive change in dough structure from strain stiffening to strain softening behavior while dough samples aged at 4 °C showed fairly close behavior with the control dough sample. FTIR spectra indicated that the relative content of β-sheet and β-turn structures decreased while the content of α-helix structure increased for all dough samples as a result of dough aging. SDS-PAGE results supported the breakdown of high molecular weight (HMW) and low molecular weight (LMW) glutenin subfractions. Aging at the higher temperature of 25 °C decreased the HMW/LMW ratio from 0.77 to 0.59, while the ratio was 0.73 for the dough aged at 4 °C which is fairly close to the control sample. Our results show that the degradation rate of gluten/starch network was triggered by aging at higher temperature, longer aging time, and natural fermentation which resulted in increasing acidity and increase in endogenous proteolytic and amylolytic activity, and also increasing gluten solubility and break down of intermolecular disulfide bonds at acid pH.