Managing biodiversity often requires making difficult trade-offs, especially when threatened species and ecosystems overlap in their distributions, and management actions to promote their persistence varies between them. Tradeoffs reflect preferences and how much decision makers are willing to give up in benefits for one objective in exchange for gains in other objectives. Despite the increase of tools for exploring trade-offs, decisions are often made without clear specification of preferences among objectives, reducing transparency and limiting clear communication of the rationale behind decisions. We used structured decision making to navigate trade-offs between ecological objectives and management costs across three conservation reserves of protected grasslands in Victoria, Australia. The objectives included four nationally listed threatened species, two nationally listed threatened ecosystems, a group of locally threatened and rare non-listed species and management costs. Alternative management strategies included various combinations of fire management and weed control. The consequences of alternatives were estimated using stochastic models, empirical data and expert judgment. Context dependent preferences were elicited using swing weighting from nine decision makers and stakeholders. While all species and ecosystems are valued, how they are weighted, and the resulting preferred management strategy is context dependent. Weights were variable across participants for all objectives. There was stronger alignment of weights for one of the ecosystems, Natural Temperate Grasslands, than other objectives. One of the threatened species, striped legless lizard, tended to be weighted higher than other ecological objectives, while management costs had the lowest weights. Stakeholder's weightings for objectives varied, however the influence on the rank order of management strategies was minimal. The structured approach to navigate trade-offs identified management strategies that best address stakeholder preferences across multiple objectives. This approach offers improvements in evidence-based decision making T. J. Regan and J. MacHunter have contributed equally to this paper.