The response of benthic habitats and organisms to bottom-contact fishing intensity is investigated in marine protected areas (MPAs) of the German EEZ in the North and Baltic Seas. We examined the current state of macrofauna biodiversity in 2020–2022. Comparative analysis for macrofauna (in- and epifauna) inhabiting nine Natura 2000 MPAs constitutes a baseline to assess the effects of bottom-contact fishing exclusion in the future. Aspects of spatial and temporal variability are briefly summarized and discussed. We provide a species list for each region, including 481 taxa, of which 79 were found in both regions, 183 only in the North Sea, and 219 only in the Baltic Sea. The Baltic Sea dataset surprisingly included higher numbers of taxa and revealed more Red List species. The share of major taxonomic groups (polychaetes, bivalves and amphipods) in species richness showed peculiar commonalities between the two regions. In the North Sea, multivariate analysis of community structure revealed significantly higher within-similarity and stronger separation between the considered MPAs compared to the Baltic MPAs. Salinity, temperature and sediment fractions of sand were responsible for over 60% of the variation in the North Sea macrofauna occurrence data. Salinity, mud fraction and bottom-contact fishing were the most important drivers in the Baltic Sea and, together with other considered environmental drivers, were responsible for 53% of the variation. This study identifies aspects of macrofauna occurrence that may be used to assess (causes of) future changes.