Dough mixing involves a combination of different deformation flows, e.g. shear and elongation. The complicated nature of mixing process makes it difficult to understand dough processing at a mechanistic level. A new Couette device allowed the effects of shear flow on the physical properties of glutenin macro-polymer (GMP) and micro-structure formation of the dough to be studied. Steady shear deformation using concentric Couette-type flow did not decrease GMP content or size of glutenin particles. Confocal scanning laser microscopy revealed the formation of interconnected gluten domains indicating the development of a gluten network. In an eccentric Couette configuration the results depended on the degree of eccentricity. A higher degree of eccentricity and a longer processing time led to considerable reduction in GMP content and size of glutenin particles. The micro-structural change in the narrow gap regions of the eccentric cell occurred early in processing, leading to a break up of large protein domains, and a microscopically more homogeneous dough. Transient high shear flow led to elongation and break up of the macroscopic gluten network. In low shear regions of the eccentric cell (wider gap settings), reformation or aggregation of protein domains was observed. Thus, the gluten aggregation–break up mechanisms are strongly influenced by the local flow profile in a conventional mixer. The impact of different types of shear flow must be taken into account in the design of dough mixers.