A new technology for reducing wheat flour toxicity for celiac disease patients through the in situ formation of gluten-chitosan interlocked self-assembled supramolecular architecture was developed. To have a deeper insight into the microstructure of this new molecular organization and its impact on the dough properties, its small and large deformation rheological properties and the macromolecular features of gluten-chitosan polymers were studied. The reduction of gluten proteins followed by spontaneous oxidation in the presence of the chitosan template in the range of 7.5:1 to 1.3:1 protein to chitosan weight ratio imposed a different reorganization of wheat flour proteins in the polymeric fraction changing conformation from homogeneous spherical molecules to polymer molecules with random-coil conformation. The polymeric fraction increased with decreasing protein to chitosan weight ratio attaining a maximum value at the 1.9:1 ratio. Moreover, the formation of the novel supramolecular architecture at this ratio allowed dough to maintain its ability to form a network after water addition and kneading showing a higher elastic and viscous moduli when compared to the control flour and the other studied formulations. It also presented a significantly higher resistance to extension, didn't inhibit the fermentation process, and retained the original dough ball shape while the dough made with the untreated flour presented a considerable extension during baking. Results show that it is possible to obtain a fully-functional wheat-based product when using a 1.9:1 protein to chitosan weight ratio with a reduced toxicity for celiac patients, opening in this way a new perspective concerning the quest for alternatives of gluten-exclusion diet.