The rheological behaviour of dough during the breadmaking process is strongly affected by the accumulation of yeast metabolites in the dough matrix. The impact of metabolites in yeasted dough-like concentrations on the rheology of dough has not been characterised yet for process-relevant deformation types and strain rates, nor has the effect of metabolites on strain hardening behaviour of dough been analysed. We used fundamental shear and elongational rheometry to study the impact of fermentation on the dough microstructure and functionality. Evaluating the influence of the main metabolites, the strongest impact was found for the presence of expanding gas cells due to the accumulation of the yeast metabolite CO2, which was shown to have a destabilising impact on the surrounding dough matrix. Throughout the fermentation process, the polymeric and entangled gluten microstructure was found to be degraded (−37.6% average vessel length, +37.5% end point rate). These microstructural changes were successfully linked to the changing rheological behaviour towards a highly mobile polymer system. An accelerated strain hardening behaviour (+32.5% SHI for yeasted dough) was promoted by the pre-extension of the gluten strands within the lamella around the gas cells. Further, a strain rate dependency was shown, as a lower strain hardening index was observed for slow extension processes. Fast extension seemed to influence the disruption of sterically interacting fragments, leading to entanglements and hindered extensibility.