Plant metabolism is characterized by a unique complexity on the cellular, tissue, and organ levels. Mathematical modeling of metabolism offers new approaches to predict, understand and modify complex plant metabolic processes. The objective of this thesis was to apply optimization-based modeling approaches to plant metabolic systems, focusing on the development of a modeling pipeline for the reconstruction, analysis and visualization of metabolic models and its application to organ-specific models of barley. The application of the reconstructed plant models allowed to verify and extend current knowledge as well as to gain new, experimentally proven, insights into barley plant metabolism. Thus, it could be shown that optimization-based analysis provides a useful alternative to traditional methods of plant metabolic network analysis.