This paper considers participatory modelling to integrate biodiversity conservation into land use planning and to facilitate the incorporation of ecological knowledge into public decision making for spatial planning. Réunion Island has experienced rapid urban and agricultural expansion, which threaten its unique biodiversity. In this context, we designed three participatory modelling sequences, involving overall 24 multidisciplinary researchers and stakeholders. The sequences aimed: (1) to map land-use and biodiversity, (2) to develop a conservation plan following systematic conservation planning principles using a spatial optimization tool (MARXAN) and (3) to simulate coupled land-use/conservation scenarios using a multi-agent system (MAS). The conservation plan confirms that priority areas for biodiversity protection are located on the coast where rapid land-use changes occur. Nevertheless, stakeholders from the urban and agricultural sector did not participate to this sequence. Indeed, conservation planning tools are useful to locate conservation priorities but they have to be designed with stakeholders to be accepted as negotiation tool. Besides, the researchers engaged in this second sequence were perceived as conservation stakeholders rather than holders of scientific knowledge. In the third sequence, the researchers involved adopted the stance of facilitating the elicitation of each stake and gathered trust from stakeholders. Overall, we conclude that the participatory development of land-use simulation models should be promoted to explore alternative scenarios for biodiversity conservation with stakeholders. In a situation of land-use conflict, a gradual and sequential participatory modelling approach should be implemented to fit into public decision-making processes.