Mapping and Assessment of Ecosystems and their Services (MAES) are central to the EU Biodiversity Strategy to 2020. Action 5 of the Strategy’s second target asks all EU member states to map and assess the state of ecosystems and their services in their national territories. Such comprehensive mapping and assessment builds on several individual tasks and their systematic integration. Therefore, an integrated and operational framework is needed, supporting and coordinating these activities. The presented framework builds on existing work done by the European Commission’s MAES Working Group and provides a clear nine-step approach including the identification of relevant questions or themes to be addressed, identification and mapping of ecosystem types, ecosystem condition and ecosystem services, their integration and dissemination of results. This framework can be used to set-up related research and development initiatives and to guide involved scientists, decision-makers and practitioners through the different steps and related tasks of the process.