Can process intensification change the future of biodiesel? presents the answers for improving biodiesel production with process systems engineering tools such as membrane reactor modeling and superstructure optimization. A novel membrane reactor model with dynamic functions of reversible and irreversible fouling and a new dynamic membrane cleaning model have been developed for biodiesel production. The models can be used to capture the cyclic behavior of the membrane reactor and identify an optimal operating cycle that balances cleaning costs and production capacity. The superstructure model is a network of different alternative options and brings the optimization of biodiesel production from equipment level to process level. An optimal route to produce biodiesel from tallow with reactive distillation and heterogenous acid catalyst is found by solving the superstructure optimization problem. The impacts of different uncertainties such as the prices of feedstock and products, and the production capacity on the total profit of a biodiesel refinery are analyzed. From the technical assessment with the superstructure, process intensification technologies such as reactive distillation are important for biodiesel production in particular and the process industry in general. The thesis discusses the potential of process intensification and digital twin applications in the energy transition of the process industries. The digital twin offers high quality and dynamic models which can be used to develop, test, and improve not only the process intensification designs but also their operating conditions. Therefore, the combination reduces the investments for prototypes and pilot plants as well as the costs of adjusting the physical equipment, allowing a prosperous future for biodiesel.