Ecosystem-based management (EBM) has been widely accepted as the new paradigm to manage marine ecosystems. Although various efforts have been made to define key components, guidelines, and principles, in support of its implementation, there is still a gap between theory and practice. To implement EBM, managers require a decision-making framework in which the values of constituents, objectives and performance measures are consistent and used to evaluate and choose between alternatives. Structured decision-making (SDM) is a systematic approach that can contribute to develop this framework for EBM. SDM was used for the on-going EBM process on the west coast of Vancouver Island, British Columbia, Canada. This case study provides insights into how SDM can be implemented for EBM, as well as some challenges and opportunities encountered during the process.