Chemical oxidizers and redox enzymes have traditionally been used to enhance the quality of baked goods. However, consumers now seek natural and clean-label ingredients, avoiding those with chemical-sounding names. Honey, a natural source of glucose oxidase (GOX), represents a promising alternative to purified enzymes for baking purposes. This study aimed to evaluate the effect of honey on the molecular structure and microstructure of gluten proteins in sourdough fermented by different lactic acid bacteria (LAB) strains. Four wheat-rye (1:1) sourdoughs were prepared, each supplemented with honey and inoculated with a different LAB strain. Additionally, two uninoculated doughs, one with honey (honey dough) and the other without (control dough), were prepared under identical conditions. Electronic paramagnetic resonance spectroscopy revealed the presence of hydrogen peroxide in honey solutions, indicating its role as an active source of GOX. Raman spectroscopy showed that honey addition altered the molecular structure of gluten by increasing the proportion of random coils at the expense of α-helix structures. This change is likely attributed to the competition between honey sugars and gluten proteins for water molecules in this system. Moreover, honey led to a decrease in the free sulfhydryl content of gluten compared to the control dough, suggesting an increase in disulfide crosslinking points. These enhanced protein-protein interactions were observed in scanning electron microscopy micrographs as a coarse gluten network composed of interconnected strands and fibrils. All LAB strains exhibited optimal acidification (pH < 4.3) in honey-supplemented sourdoughs, promoting the hydrolysis of gluten proteins into smaller fragments. Overall, honey-supplemented sourdoughs showed a gradual increase in the β-sheet content while decreasing the proportion of random coils over time. This trend suggests that the polypeptide fragments interacted through interchain hydrogen bonds, leading to a more ordered structure, which likely contributes to providing dough with good baking aptitude.