Environmental sustainability in manufacturing has been experiencing increasing attention in practice and academia over the last decades. Manufacturing companies strive to improve their eco-efficiency, which is commonly understood as delivering high value products at lower cost and environmental impact. They need tools and methods to translate this strategic goal onto the operational shop floor level. This paper presents a procedure for optimizing the eco-efficiency of production systems, supported by a discrete-event material flow simulation model. Its application is shown in a case with a company from the Swiss consumer goods industry.