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METAPLANTCODE presents a unique collaborative and transnational approach to test, optimize, harmonize and recommend best practices for plant metabarcoding for samples with varying degrees of species complexity, contamination and DNA degradation using case studies across Europe. The innovative combination of accelerated molecular plant monitoring and the integration of diverse biodiversity data with optimized and automated pipelines will close knowledge gaps on the state of biodiversity, interdependencies and dynamics. The new techniques are suitable for large-scale, long-term, high-throughput monitoring and enable biodiversity surveys on a scale and with a precision that was previously unattainable.