Research Highlights: The developed National Set of Indicators for the Mapping and Assessment of Ecosystems and their Services (MAES) implementation in Greece at the national level sets the official, national basis on which future studies will be conducted for MAES reporting for the achievement of targets within the National and the European Union (EU) biodiversity Strategy. Background and Objectives: Greece is currently developing and implementing a MAES nation-wide program based on the region’s unique characteristics following the proposed methodologies by the European Commission, in the frame of the LIFE-IP 4 NATURA project (Integrated actions for the conservation and management of Natura 2000 sites, species, habitats and ecosystems in Greece). In this paper, we present the steps followed to compile standardized MAES indicators for Greece that include: (a) collection and review of the available MAES-related datasets, (b) shortcomings and limitations encountered and overcome, (c) identification of data gaps and (d) assumptions and framework setting. Correspondence to EU and National Strategies and Policies are also examined to provide an initial guidance for detailed thematic studies. Materials and Methods: We followed the requirements of the EU MAES framework for ecosystem services and ecosystem condition indicator selection. Ecosystem services reported under the selected indicators were assigned following the Common International Classification of Ecosystem Services. Spatial analysis techniques were applied to create relevant thematic maps. Results: A set of 40 MAES indicators was drafted, distributed in six general indicator groups, i.e., Biodiversity, Environmental quality, Food, material and energy, Forestry, Recreation and Water resources. The protocols for the development and implementation of an indicator were also drafted and adopted for future MAES studies in Greece, providing guidance for adaptive development and adding extra indicators when and where needed. Thematic maps representing ecosystem services (ES) bundles and ES hotspots were also created to identify areas of ES importance and simultaneously communicate the results at the national and regional levels.