Plants, through their autotrophic capacity, are the driving force behind terrestrial ecosystems. Alarmingly, two out of five plant species face extinction, which may affect other organisms. The method of metabarcoding DNA in plants, which involves analysing environmental DNA (eDNA) to identify taxa, can be standardised and automated, making it suitable for large-scale, long-term, high-throughput monitoring. This technique allows biodiversity surveys to be conducted on a scale and with an accuracy that was previously impossible. In Europe, nature conservation initiatives are based on species presence, and indicator species form the basis for decision-making in conservation plans. However, public and private stakeholders need fast, accurate and cheap methods to monitor plant biodiversity. The transnational and transdisciplinary project METAPLANTCODE aims to test and optimise pan-European case studies on DNA metabarcoding, provide best practice recommendations, optimise data analysis methods for species identification and create user-friendly reference databases to be implemented in European and national infrastructures, in collaboration with BIOSCAN Europe, ELIXIR communities, etc.The project will identify existing gaps, publish best practice documents on the FAIR publication of plant metabarcoding data to the GBIF and INSDC databases and implement ELIXIR-compliant multimodal DL models in new tools for stand-alone metabarcoding analyses using different data sources. The project will also improve the accuracy of species identification based on GBIF and metadata (GBIF, EUNIS, Biolflor, through DNA sequence data, text data, taxonomic classification datasets and ecological analyses) and map/introduce regional, national and international vascular plant checklists, redlists and floras in the Catalogue of Life (COL) through COL ChecklistBank. In addition, the taxonomic and floristic literature will be semantically enriched with new entity recognition and relationship extraction modules to support improved species identification by domain-specific descriptive/phenotypic features (e.g. habitats, traits, soil characteristics, biotic interactions). An interface will be provided to link taxonomic names to methods, to identify homonyms and synonyms, and to facilitate conversion and annotation of flora, red lists and ecological treatments. All METAPLANTCODE products will be available following FAIR+ principles at the end of the project. The project will support knowledge transfer with associated partners and stakeholders from the outset. Relevant stakeholders will be identified, priorities determined, communication channels established, all of which will be monitored and revised as necessary. Extensive stakeholder engagement, training and outreach efforts will be undertaken to ensure that in the future DNA metabarcoding in plants becomes a routine standard for biodiversity monitoring in Europe and beyond.