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. This article presents the prototype of a material flow based optimization tool. Numerical results on the convergence of the implemented optimization algorithms are provided. 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.