Lactobacillus amylolyticus L6, a potential probiotic rich in glycosidases like maltogenic amylase (MA), may be suitable for bread fermentation. This study investigated the texture, moisture migration, starch retrogradation, microstructure, volatile compounds, and organoleptic properties of L6 whole-wheat sourdough bread (L6B) before and after storage at 4 °C for 7 days. Chemical acidifier whole-wheat sourdough bread (CB), commercial MA whole-wheat bread (MB), and normal whole-wheat bread (NB) were used as controls to reveal the anti-staling properties and flavor characterizations. The results showed that freshly baked L6B presented the lowest hardness (362.27 g), increasing to 1449.87 g after storage, which was lower than NB (2198.94 g) and CB (1999.26 g), but higher than MB (1025.24 g). L6B consistently possessed the highest total water content (8611.67 and 7693.57 a. u. for fresh and stored bread, respectively) and bound water proportion (19.61% and 15.60%). Moreover, the retrogradation enthalpy of stored L6B (3.57 J/g) was larger than that of MB (2.54 J/g), with the lowest relative crystallinity (7.17%) and recrystallization rate (28.04%). The microstructure of dough with L6 sourdough exhibited an organized fibrous and lamellar gluten matrix, more pores, and smaller starch granules. Additionally, L6B accumulated more octanoic acid, ethyl ester, hexanoic acid, ethyl ester, and nonanal, contributing floral, fruity, and fatty flavors. Sensory evaluation indicated that L6B possessed the highest overall acceptability, being especially softer, with pleasant sourness and aroma. Overall, whole-wheat bread fermented with L6 shows promising potential, exhibiting an anti-staling capability comparable to bread with MA, enhanced organoleptic properties, and flavor.