An ecosystem approach is widely seen as a desirable goal for fisheries management but there is little consensus on what strategies or measures are needed to achieve it. Management strategy evaluation (MSE) is a tool that has been widely used to develop and test single species fisheries management strategies and is now being extended to support ecosystem based fisheries management (EBFM). We describe the application of MSE to investigate alternative strategies for achieving EBFM goals for a complex multispecies fishery in southeastern Australia. The study was undertaken as part of a stakeholder driven process to review and improve the ecological, economic and social performance of the fishery. An integrated management strategy, involving combinations of measures including quotas, gear controls and spatial management, performed best against a wide range of objectives and this strategy was subsequently adopted in the fishery, leading to marked improvements in performance. Although particular to one fishery, the conclusion that an integrated package of measures outperforms single focus measures we argue is likely to apply widely in fisheries that aim to achieve EBFM goals.