The Monarch butterfly eastern population (Danaus plexippus) is in decline primarily due to habitat loss. Current habitat restoration programs focus on re-establishing milkweed, the primary food resource for Monarch caterpillars, in the central United States of America. However, individual components of the Monarch life cycle function as part of an integrated whole. Here we develop the MOBU-SDyM, a migration-wide systems dynamics model of the Monarch butterfly migratory cycle to explore alternative management strategies’ impacts. Our analysis revealed that concentrating milkweed growth in the central region increases the size of the overwintering colonies more so than equivalent growth in the south region, with growth in the northern region having a negligible effect. Systems dynamics’ analytical and computational strengths provided us with new avenues to investigate the Monarch’s migration as a complex biological system and to contribute to more robust restoration policies for this unique species.