Material flow analysis (MFA) becomes more and more an important instrument to support environmental protection and sustainable development. Often, a special approach, life-cycle assessment (LCA), is put on the same level with material flow analysis. Based on the industrial ecology or industrial metabolism paradigm (Fischer-Kowalski 1998, Fischer-Kowalski and Hüttler 1999), we interpret material flow analysis in a broader sense. That makes it possible to simulate, to analyze and, as a subsequent step, to optimize multi-product systems. This contribution shows how simulation and optimization can utilized in the field of material flow analysis. It can be shown that the different approaches are not alternatives. Rather, it is possible to combine them in order to provide a flexible MFA tool-chain.