The volume-spanning network formed by gluten during breadmaking is crucial in the production of high-quality bakery products. Zein proteins are also capable of forming a protein network under specific conditions. Vibrational (Fourier transform infrared spectroscopy (FTIR) and Raman scattering) and fluorescence spectroscopy are powerful, non-invasive techniques capable of assessing protein structures and interactions. The main objective of this project was to explore the suitability of these techniques to study zein and gluten structures and interactions in complex dough systems. The dough samples were prepared by mixing 20 w/w% of protein (with different proportions of zein and gluten) and 80 w/w% of corn starch. The tyrosine (Tyr) fluorescence emission peak (λexc = 280 nm) was still present even in those zein-gluten samples containing the highest gluten concentration and lowest zein concentration. This suggests that the Tyr moieties (stemming from zein) are not in close proximity to tryptophan (Trp) of gluten and their fluorescence is not quenched efficiently. Raman scattering results also showed the presence of different Tyr residues, exposed and buried, as well as different conformations of disulfide bridges, in zein and gluten samples. Based on the results from spectroscopic measurements and scanning electron microscopy (SEM), two distinct network structures composed of gluten and zein were identified in the mixed dough systems. The present work illustrates how complementary vibrational (Raman scattering and FTIR) and fluorescence spectroscopy methods can be combined to non-invasively assess protein structure and interactions in a complex food matrix.