Biological invasions threaten biodiversity worldwide, especially on tropical Islands such as Reunion Island where the largest area of intact vegetation occurs within the Mascarene's archipelago. With the impetus of the local government, we initiated a partnership between scientists and managers to address the management of invasive alien plant species on the island. This study aims to map biodiversity priority areas and to prioritise alien plant clearing on the island. We first established a conceptual framework shared by all partners. We then combined all existing data on habitats, both threatened and endemic species, and the distribution of alien plant species using expert knowledge where necessary. We developed a decision-making process using Zonation, a conservation planning tool, to identify biodiversity conservation priorities. Conservation priority areas were selected with the aim of maximising biodiversity levels in areas slightly invaded. The criteria used to identify priority areas for the control of alien plant species included clearing costs, accessibility, and the history of previous management programmes. A total of 60,303 ha were identified as conservation priority areas, 30% of which are not considered to be invaded. Based on biodiversity and implementation issues, we identified plant clearing priority areas that highlighted invasion fronts. Priorities identified helped to spatially re-align existing clearing operations. This study, conducted jointly by managers, decision-makers and scientists has allowed the identification of priority areas concerning the control of alien plants and their implementation thereafter. The engagement of stakeholders at each relevant step of a conservation project is essential in guiding decision making, and the future implementation.