Proton-exchange membrane fuel cells (PEMFC) offer a promising energy generation alternative for a wide range of technologies thanks to their ecological friendliness and unparalleled efficiency. At the heart of these electrochemical cells lies the membrane electrode assembly with its most important energy conversion components, the Proton Exchange Membrane. This component is created through the use of printing techniques and Nafion inks. The physicochemical properties of the ink, such as its viscosity under shear, are critical for the finished product. In this work we present non-equilibrium Molecular Dynamics simulations using a MARTINI based coarse-grained model for Nafion to understand the mechanism governing the shear viscosity of Nafion solutions. By simulating a Couette flow and calculating density maps of the Nafion chains in these simulations we shed light on the process that leads to the experimentally observed shear thinning effects of Nafion solutions under flow. We observe rod-shaped Nafion microstructures, 3 nm in size on average, when shear flow is absent or low. Higher shear rates instead break these structures and align Nafion strands along the direction of the flow, resulting in lower shear viscosities. Our work paves the way for a deeper understanding of the dynamic and mechanical properties of Nafion including studies of more complex CL and PEM inks.