Mixed-integer supply chain models typically are very large but are also very sparse and can be decomposed into loosely coupled blocks. In this paper, we use general-purpose techniques to obtain a block decomposition of supply chain instances and apply a tailored penalty alternating direction method, which exploits the structural properties of the decomposed instances. We further describe problem-specific enhancements of the algorithm and present numerical results on real-world instances that illustrate the applicability of the approach.