The Biodiversity Digital Twin (BioDT) initiative is a pioneering effort aimed at enhancing biodiversity monitoring, conservation strategies, and policy decision-making across the European Union. By leveraging high-performance computing, artificial intelligence, and real time ecological data, BioDT aligns with EU policies, such as the EU Biodiversity Strategy for 2030, the EU Green Deal, and the European Data Strategy. The initiative offers a novel approach to biodiversity assessment, yet its full potential remains constrained by technical, infrastructural, and regulatory barriers. Key challenges include limited geographical coverage of remote sensing technologies, gaps in species data and inadequate early detection systems for invasive species. Furthermore, issues related to data interoperability and integration, including the absence of standardised DNA metabarcoding protocols and insufficient cross border coordination, hinder seamless data-driven biodiversity management. Additionally, integrating BioDT with existing EU digital and data infrastructures is complicated by limited computational resources, ethical concerns regarding AI-driven biodiversity analysis, and the lack of standardised access guidelines for high-performance computing (HPC) resources such as EuroHPC and LUMI. To address these issues, this policy brief presents a set of targeted recommendations. These include establishing an EU Biodiversity Observatory to integrate real-time monitoring with BioDT, enforcing EU-wide standards for biodiversity data management, and ensuring long-term access to HPC resources for ecological modelling. Additionally, harmonising AI governance frameworks for biodiversity applications and improving accessibility to critical land-use and trait data will be essential for ensuring BioDT’s effectiveness. With proper policy alignment, BioDT can become a cornerstone of evidence-based biodiversity conservation, driving better decision making and fostering sustainable ecological management practices in Europe.