The shelf-life of bread is influenced by flour components, such as starch, composed of amylose and amylopectin. The aim was to test the effect of different balances of N (45, 90, 135 kg/ha) and P (48, 96 kg/ha) fertilizers on the flour characteristics and consequently the shelf-life of PDO Tuscan bread, stored in different modified atmosphere packaging (Ar, N2, Air). The amylose and phytochemical compounds were increased by N and decreased by the addition of P, but excessive doses of N (135 kg/ha) had a negative effect on flour quality. In the bread, the study highlighted the tendency of N2 and Ar, as storage filler gases, to reduce water loss, slow down the staling process, and prolong shelf-life. However, the most significant influence on shelf-life was related to the different fertilizations of wheat. In fact, when N was present in equal dose to P (90/96 or 45/48 kg/ha) or slightly higher (90/48 kg/ha), the bread tended to last longer over time. Instead, when these ratios were unbalanced in favor of N (135/48 or 135/96 kg/ha) and in favor of P (45/96 kg/ha), the shelf-life decreased considerably.