The establishment of Natura 2000, the European Union’s network of protected areas, has been a challenging process and has caused a variety of conflicts. These conflicts are related to contradictory stakeholder interests and perceptions, as well as to procedural issues and feelings of exclusion, especially by concerned local land user groups. To prevent further conflict, local participation has been stressed as an important tool to increase the inclusiveness of Natura 2000 and its acceptance among land users. In this paper, we present an analysis of participation practices related to the Natura 2000 implementation processes in six EU member states. Based on material collected from semi-structured interviews and document analysis, we describe the organisational settings of the participatory processes, focusing, among other things, on the type of participants involved, the level and intensity of their involvement, and the goal of participation. In addition, we also describe the local context in which the participation processes have been embedded. Finally, we assess the outcomes of the participatory processes in terms of their impact on forest and nature conservation management practices. Our results show that local participation practices were shaped not just by the Natura 2000 policy, but also by the history of the area, including, for example, earlier conflicts among the local actors. We also show that although the participation process leads to a greater acceptance of the Natura 2000 policy, this does not relate to significant changes in management practices among local actors. These findings, however, do not suggest that participation is irrelevant. Rather, we conclude that participation involves context-dependent, localised learning processes that can only be understood by taking the historical socio-economic and institutional context in which they are situated into account.