Integrating ecosystem services into ecosystem-based management (EBM) is currently one of the most relevant challenges for management. For that purpose, it is necessary to depict the relationships established between ecosystems and society considering the delivery, use and governance of ecosystem services. One effective way of doing so involves collaboration between researchers, who scientifically study the system, and managers, who have specific experience and technical knowledge. With this aim, we held two workshops in 2011 in the National Parks of Doñana and Sierra Nevada, Andalusia (Spain), with researchers and managers from the protected areas at different organizational levels: local, regional and national. Taking the participative mental model technique as an inspiration, we developed a tool that was used as a means to allow a holistic analysis of ecosystem services from an interdisciplinary and participative perspective. We found that participatory mental models, help integrating ecosystem services into EBM as it includes stakeholders’ proposals and knowledge. For the implementation of ecosystem services for management, we discuss the necessity of navigating a process that requires considerable changes, not only in using new concepts such as ecosystem services, but also in the management structures that govern the services. This process would require closer interaction between citizens, researchers and managers, and the creation of new participation spaces that include ecosystem service beneficiaries located beyond protected areas.