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Natura 2000 sites are expected to assure the long-term survival of Europe's most valuable and threatened species and habitats. It follows that successful management of the sites is of great importance. Next to goal attainment, cost-effectiveness is increasingly recognised as a key requirement for gaining social and political acceptance for costly conservation measures. We identify and qualitatively examine issues of cost-effectiveness related to the design and implementation of management measures in Natura 2000 sites in Finland, Germany, the Netherlands and Poland. Given the wide variety of management design and implementation options within the four countries, our study is purely of an exploratory nature. We derive recommendations for improving the cost-effectiveness of management in Natura 2000 sites and for future research. Examples of policy recommendations include guaranteeing the availability of funds for longer periods, and ensuring the appropriate allocation of funds between the different tasks of designing and implementing management plans. Further research should examine the cost-effectiveness of controversial suggestions such as, for example, more tailored payment schemes for conservation measures that result in higher ecological outputs but are costly to administer. Moreover, more research is needed to better understand how rules for administrations, as well as rules and governance structures for tasks within administrations, should be designed.