Information on changes in the area of different ecosystems is needed in order to establish an accounting system for ecosystem conditions and services. Currently, there are no comprehensive field mappings for the German federal states that obey a uniform mapping system. To create a nationwide “ecosystem accounting”, it is necessary to develop a uniform system of ecosystem classifications that can consistently deal with diverse nationwide data sources on the extent and condition of ecosystems, some of which use their own forms of classification. Against this background, we present a concrete proposal on how to combine and blend GIS land-use and ecosystem data that is compatible with EU-wide approaches with other regularly collected data sources, for example, from sample-based surveys, so as to generate a complete, updatable picture of the state of Germany’s ecosystems. The area shares of ecosystem types (ETs) can be shown in maps. Allocation tables with different classes or levels (layers) enable an ecosystem extent accounting, which are used to help draw up balances (area balance, status balance, service balance) and can be further detailed, depending on the task at hand. First results and trends of areal changes of main and sub-ecosystem types in Germany, based on the proposed classification system, are presented and discussed. However, the brevity of the considered timeframe (the three periods 2012-2015-2018) does not yet allow us to pinpoint trends or migratory movements, as these may be masked by methodological changes in the classification of land use and land cover. Nonetheless, the presented system for accounting changes in ecosystem areas should be continued and developed in the future in order to create a useful tool for biodiversity monitoring in Germany.