Biodiversity represents one of the most controversial areas of environmental governance. Objectives: Compliance with the EU regulatory framework is contained in the Habitats Directive (92/43/EEC) and in the designation of special areas of conservation which has prompted contestation in relationships between public authorities, farmers, and local landholders across all levels of governance. Methodology: Using Matland’s ambiguity-conflict model as a lens to view the implementation experience, the discussion uses official documentation and literature sources to explore Ireland’s compliance with EU biodiversity regulation with reference to peatlands. Results: This article uses the case of Ireland to explore inadequate implementation which led to prolonged legal proceedings culminating in an unfavourable judgement against the Irish state on 29th June 2023. In Case C-444/21 the Court of Justice of the European Union (CJEU) ruled that Ireland failed to fulfil its obligations under the directive, namely the appropriate designation of a Natura 2000 network of sites for important habitat and a protection regime for them. Central to Irish debates on the habitats directive is the protection of raised bogs which has resulted in considerable conflict, politicisation, and prolonged negotiations between peat-cutters and public authorities at national and local levels. Conclusions: The discussion highlights the difficulties in changing ingrained attitudes and practices for managing nature conservation in privately owned land and in securing collaborative engagement with stakeholders.