Our study is part of a multi-disciplinary research project aimed at stimulating debate among researchers and local managers. The central question of this multi-disciplinary research project was to better understand and manage high biodiversity value open habitats threatened with shrub encroachment and landscape closure, a common problem throughout Europe. Here, we study shrub encroachment and its impact on biodiversity conservation in Mount Ventoux, a MAB Biosphere Reserve located at the southernmost tip of the French Alps. We show how using a multi-agent modelling approach provide a valuable framework to confront two potentially conflicting conservation efforts in this mountain Mediterranean landscape, that of the within-species diversity of a tree (Abies alba, the European silver fir) and that of an endangered species (Vipera ursinii ursinii, the Orsini viper). A companion modelling approach - approach which aims at transmitting and sharing knowledge, methods and tools that help understand and strengthen the collective decision making process of stakeholders sharing a common resource - was used in order to collectively represent the main activities underway on the mountain and to have a tool to address both open landscapes rehabilitation and restoration of forest environments. The co-construction of the model allowed us to build a shared representation of the territory under study and to develop and compare alternative management scenarios with local stakeholders, both to evaluate their impact on biodiversity and to provide information for forest and grazing management practice.