Climate-driven changes in ocean currents have facilitated the range extension of the long-spined sea urchin (Centrostephanus rodgersii) from Australia’s mainland to eastern Tasmania over recent decades. Since its arrival, destructive grazing by the urchin has led to widespread formation of sea urchin ‘barrens’. The loss of habitat, biodiversity and productivity for important commercial reef species in conjunction with the development of an urchin fishery has led to conflicting objectives among stakeholders, which poses complex challenges for regional management. Stakeholder representatives and managers were engaged via a participatory workshop and subsequent one-on-one surveys to trial a structured decision-making process to identify effective ecosystem-based management strategies. We directly and indirectly elicited each stakeholder’s preferences for nine alternative management strategies by presenting them with the 10-year consequences of each strategy estimated from an ecosystem model of Tasmanian reef communities. These preferences were included in cost-effectiveness scores that were averaged (across stakeholders) to enable strategy ranking from most to least cost-effective. Rankings revealed strategies that included sea urchin removal or translocation of predatory lobsters were the most cost-effective. However, assessment of stakeholders’ individual cost-effectiveness scores showed some disparity among stakeholders’ preferences in high ranking strategies. Additionally, evaluating inconsistencies within some stakeholders’ scores that included direct or indirect preferences revealed conflicting objectives and cognitive bias as the most plausible explanations for these inconsistencies. Our study illustrates how structured decision-making can effectively facilitate ecosystem-based management by engaging stakeholders step-by-step towards management strategy implementation, identifying psychological barriers to decision-making and promoting collective learning.