The key to many chemical and energy conversion processes is the choice of the right molecule, for example, used as working fluid. However, the choice of the molecule is inherently coupled to the choice of the right process flowsheet. In this work, we integrate superstructure‐based flowsheet design into the design of processes and molecules. The thermodynamic properties of the molecule are modeled by the PC‐SAFT equation of state. Computer‐aided molecular design enables considering the molecular structure as degree of freedom in the process optimization. To consider the process flowsheet as additional degree of freedom, a superstructure of the process is used. The method results in the optimal molecule, process, and flowsheet. We demonstrate the method for the design of an organic Rankine cycle considering flowsheet options for regeneration, reheating, and turbine bleeding. The presented method provides a user‐friendly tool to solve the integrated design problem of processes, molecules, and process flowsheets.