We consider optimal control problems that have binary-valued control input functions and a perimeter regularization. We develop and analyze a trust-region algorithm that solves a sequence of subproblems in which the regularization term and the binarity constraint are relaxed by a non-convex energy functional. We show how the parameter that controls the distinctiveness of the resulting phase field can be coupled to the trust-region radius updates and be driven to zero over the course of the iterations in order to obtain convergence to points that satisfy a first-order optimality condition of the limit problem under suitable regularity assumptions. Finally, we highlight and discuss the assumptions and restrictions of our approach and provide the first computational results for a motivating application in the field of control of acoustic waves in dissipative media.