Material flow networks are a specific technique for material flow analysis. Software tools based on this method have been used by many companies to analyze and improve complex production systems. While their intuitive modeling approach strongly enhances the identification of optimization potentials, automatic model optimization is not yet possible. The KOMSA project has closed this important methodological and instrumental gap. This article presents the developed prototype of a material flow-based optimization tool. We provide numerical results on the convergence of the implemented optimization algorithms. The added value of integrating optimization with material flow analysis is illustrated by applying the software tool to a real optimization problem from the waste industry.