Conservation of biological diversity, a goal institutionalised through international agreements such as the Convention on Biological Diversity, or the Habitats Directive in Europe, has important implications for the management of all natural resources, as it requires a re-arrangement of management practices in a multi-faceted fashion. While protected areas may contribute to well-being globally, they might thus impose disproportionately high costs at the local level. This led us to evaluate processes and outcomes of policies governing biological diversity not only in terms of how just, but in terms of how fair they are. With a particular focus on the conflicts arising among different groups of stakeholders when establishing protected areas for biodiversity conservation we shed light on the role fairness plays for effective management which we introduce as problem of complex social dilemma. The framework developed is applied in the discussion of two case studies: the first one considers biodiversity protection in the Alpine region Verwall, Austria, highlighting the importance of procedural fairness; the second case study considers the Small Island of Braila, Romania, highlighting the relevance of distributional fairness. We conclude that if biodiversity conservation is hampered by complex social dilemma the success of partnership approaches may critically depend not only on aspects of distributional and procedural fairness but also on trust in effective monitoring and sanctioning systems that counteract the underlying social dilemma and support a fair sharing of costs and benefits that meets the subjective fairness appraisals of the partners.