Plastic profile extrusion—a manufacturing process for continuous profiles with fixed cross section—requires a complex and iterative design process to prevent deformations and residual stresses in the final product. The central task is to ensure a uniform material velocity at the outlet. To this end, not only the geometry of the flow decisively influences the quality of the outflow but also the temperature profile along the flow channel wall. It is exactly here that this work contributes by presenting a novel design approach for extrusion dies that will allow for optimal temperature profiles. The core of this approach is the composition of the extrusion die through microstructures. The optimal shape and distribution of these microstructures is determined via shape optimization. The corresponding optimization procedure is the main topic of this article. Special emphasis is placed on the definition of a suitable, low-dimensional shape parameterization. The proposed design-framework is then applied to two numerical test cases with varying complexity.