In this contribution, a methodology for the optimal design of chemical reactors based on the best reaction route in the thermodynamic state space is proposed. This route is obtained by tracking a fluid element on its way through the reactor and manipulating the fluxes into this element. Instead of choosing the reactor design a priori and optimizing the free parameters of the chosen reactor setup, an innovative reactor design is developed based on the optimal flux profiles. Besides classical reactor concepts, this methodology is suited to investigate the potential of different process intensification options such as integration of reaction, cooling and separation in a single apparatus, or the application of high interface areas for heat and mass transfer. The methodology is exemplarily illustrated for the development of a new SO2 oxidation reactor. The residence time as an example for a meaningful objective is minimized, and a reduction of 69% compared to the optimized technical reference case is achieved.