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Abstract The theoretical concept of the ecosystem approach (EA) aims at assessing ecosystem function based on integrative assessments of multiple levels of biological organization. Since the United Nations Convention on Biological Diversity in 1992, the EA has been increasingly integrated into environmental policy and legislation, but to date, its practical implementation remains vague with a lack of universal guidelines and concrete recommendations for its use across ecosystem boundaries. On the basis of a review of scientific literature, worldwide environmental legislation and existing monitoring approaches, we identified the most important factors which hamper the feasibility of the EA. We propose a generally applicable methodology for implementing the EA in ecological and environmental monitoring across different ecosystems and habitat types. Successful application of the EA largely depends on adequately standardized and synchronized sampling designs for all abiotic and biotic components, appropriate depth of taxonomic identification, and sufficient spatial and temporal replication. The proposed step‐by‐step guidelines for using the EA are valid across ecosystem types, geographic regions, and for a variety of data types, making them promising tools for ecological monitoring.