In order to maximize the profit of a biodiesel production plant, one has to decide the numbers of unit productions and the values of controller parameters. This study addresses the problem by examining various control loops and process configuration within a process superstructure. The problem is formulated as a dynamic Mixed Integer Nonlinear Problem and is subsequently solved by using the Dynamic Operability Framework. This approach yields the process configuration and the controller structure that gives the maximum profit for a 200 liters biodiesel batch mini-plant.