The research objective was to investigate the morpho-rheological, chemical, and structural changes of dough and Neapolitan pizza TSG as the leavening time varies and to evaluate their effects on the digestibility of starch and on the formation of acrylamide during baking. Pizza dough leavening was monitored for 48 h at 22 °C/80% RH, and the analyses were conducted at selected leavening times (0, 4, 8, 16, 24, and 48 h). It was observed that in 30 h the volume tripled and the viscoelastic dough relaxed in the first 4 h, as evidenced by the lower value of the relaxation percentage “a” and the higher rate of decay “b”, associated with a high value of the compression work, indicating the presence of a very strong gluten mesh. In the following hours, the dough lost elasticity, and in fact, the G’ modulus decreased due to the weakening of the weak interactions between the gluten proteins and the starch. This suggests that a long leavening improved the extensibility of the pizza disc, facilitating the action of the pizza maker. Thermal (TGA and DSC) and morphological (SEM) analyses evidenced the highest water removal rate from the dough, a wider starch gelatinization temperature range, a ∆H of 0.975 ± 0.013 J/g, and a more open and weak gluten structure in dough balls leavened for 16 h. As the leavening time increased, both dough and pizza base samples showed an increase in reducing sugars and free amino groups, while the rapidly digestible starch decreased in the dough following the metabolism of the yeasts and increased in the pizza base due to the starch gelatinization that occurs during baking, which makes it much more susceptible to α-amylase. Finally, the levels of acrylamide remained at the same values despite the higher availability of reducing sugars and its precursors during leavening.