This paper presents a methodology based on multiobjective evolutionary optimization and a phase control scheme to design a microwave heating applicator for water sterilization. The optimization problem is formulated in terms of two objective functions: one to maximize the amount of water and the other to minimize the energy spent. The device is modeled as a lossy dielectric multilayer irradiated by two microwave sources. The phase control is done by allowing one of the sources to move. By applying the developed methodology, an efficient applicator is obtained.