The ecosystem-based fisheries management (EBFM) framework has a solid theoretical justification and has been embraced in principle by many regions; yet, systematic implementation remains a challenge. In regions with strong governance, single-species stock assessment and management has been successful in ending overfishing and maintaining stocks near levels that produce maximum catches. However, considering species in isolation and recognizing a limited set of management objectives leads to systemic inefficiencies, incentivizes waste and generates unintended consequences. To avoid undesirable outcomes, human values and needs must be positioned at the forefront of management, system-level objectives must be identified, and management actions must be systematically evaluated to ensure they are contributing to those larger objectives. Such processes, when implemented transparently, will lead to reduced conflict and improved stakeholder support for governance and should greatly facilitate long-term management. We argue here that, regardless of the management framework adopted, we inherently manage at the ecosystem level—albeit sometimes “blindly”—and that increased attention to ecosystem objectives and trade-offs will improve management outcomes.