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Marine protected areas (MPAs) represent the main tool for halting the loss of marine biodiversity. However, there is increasing evidence concerning their limited capacity to reduce or eliminate some threats even within their own boundaries. Here, we analysed a Europe-wide dataset comprising 31,579 threats recorded in 1692 sites of the European Union's Natura 2000 conservation network. Focusing specifically on threats related to marine species and habitats, we found that fishing and outdoor activities were the most widespread threats reported within MPA boundaries, although some spatial heterogeneity in the distribution of threats was apparent. Our results clearly demonstrate the need to reconsider current management plans, standardise monitoring approaches and reporting, refine present threat assessments and improve knowledge of their spatial patterns within and outside MPAs in order to improve conservation capacity and outcomes. Unlabelled Image • Recreational activities and fishing are the main threats affecting European MPAs. • The majority of the threats occur/act both inside and outside the boundaries of the MPAs. • There is heterogeneity in the distribution of threats across European countries. • Standardised monitoring and assessments are needed to improve conservation capacity and outcomes. [ABSTRACT FROM AUTHOR]