Context Invasive alien species have been pointed out as an important driver of biodiversity loss. Many policy responses are being developed to address this threat. Protected areas often represent and preserve hotspots of biological diversity and ensure the maintenance of ecosystem services crucial to human livelihoods. The impact of biological invasions can be particularly severe in protected areas and their occurrence and impact in such areas is an important element of the risk they pose. To address this, there is a need for data on the occurrence and extent of alien species invasions in protected areas. Description This dataset contains species occurrence and occupancy in protected areas of the Natura2000 network in Belgium (Special Conservation Areas sensu Habitat Directive and Special Protection Areas sensu Bird Directive). The dataset was generated using the Belgian occurrence cube at species level and the Belgian occurrence cube for non-native taxa (both containing GBIF data aggregated using Oldoni et al. 2020), the 1x1km EEA reference grid and the Natura2000 protected areas shapefiles from the European Environment Agency. Data are grouped by protected area (SITECODE), year (year) and (infra)species (taxonKey, speciesKey). For each group, it provides the number of occurrences found in GBIF (n), the area of occupancy (aoo: number of 1 km2 squares), the coverage (coverage: % of 1 km2 squares), the minimum coordinateUncertaintyInMeters (min_coord_uncertainty), and the alien status (is_alien) based on the Global Register of Introduced and Invasive Species - Belgium. For infraspecific taxa in the latter, the alien status of the species is looked up and included. The dataset is built on open science principles and intended to be completely reproducible: The input data are publicly available on Zenodo, with the download DOIs listed in the related identifiers of this dataset package. The code to process the data is publicly available and documented on GitHub. Files protected_areas_species_occurrence.csv: number of occurrences (n), area of occupancy (aoo) and coverage of taxa (taxonKey) in Natura2000 areas of Belgium (SITECODE). Other columns included: speciesKey (for species is speciesKey = taxonKey), SITETYPE containing the site type of the Natura2000 area (one of A, B or C), min_coord_uncertainty with the lowest coordinate uncertainty in meters, is_alien containing the alien status (TRUE or FALSE) and remarks containing, if present, the infraspecific alien taxa whose occurrences contribute to the calculated aoo (only for species). protected_areas_species_info.csv: taxonomic information of taxa in protected_areas_species_occurrence.csv as retrieved from GBIF Backbone Taxonomy. Columns: taxonKey, speciesKey, scientificName, kingdom, phylum, order, class, genus, family, species, rank and includes. The latter contains the infraspecific taxa and synonyms whose occurrences contribute to the number of occurrences at species level. protected_areas_metadata.csv: protected area information for areas included in protected_areas_species_occurrence.csv. Columns: SITECODE as in protected_areas_species_occurrence.csv (BE*******), SITENAME containing the name of the protected area, SITETYPE as in protected_areas_species_occurrence.csv, flanders, wallonia and brussels containing whether the area is situated respectively in Flanders, Wallonia or Brussels-Capital Region (TRUE or FALSE). Field codes are in line with EEA element definitions for Natura 2000 sites. Potential use of the dataset Currently, there is no comprehensive reporting system for invasive alien species in Natura 2000 sites. This dataset provides a baseline as to which species occur in which protected area. We envisage this dataset can be an interesting starting point for various types of analyses on alien species in protected areas in Belgium, but that it can also be used in complement to other data on alien species in protected areas to study more general patterns. Some examples of research questions: Which protected areas are most invaded by alien species Which alien species are most distributed in protected areas and which traits do they have How does the proportion of alien species in protected areas change in time How does the occurrence/occupancy of alien species in protected areas match lists of regulated species (e.g. Union List, EPPO lists) To what extent can the network of protected areas contribute to providing safe refuge to native species from the impacts of invasive alien species How widespread are the impacts of certain alien species on protected areas Acknowledgements This work has been funded under the Belgian Science Policies Brain program (BelSPO BR/165/A1/TrIAS), the European Union's LIFE program (LIFE19 NAT/BE/000953 - LIFE RIPARIAS).