Protected areas aim to conserve and restore populations of target species and their habitats, but it is challenging to quantify their effectiveness. Assessments of protected area effectiveness require long-term monitoring data, which are rarely available for all target species. We aimed to evaluate the usefulness of semi-structured citizen science data to derive population trends of target species, and use these to assess the effectiveness of EU Special Protection Areas (SPA). We derived occupancy trends for 42 target species across the SPA network of Germany over a 11-year period. We found that 62 % of the target species were more likely to occur in SPA than outside, especially when these sites also comprised parts of other types of protected areas. 17 % of the species showed more positive occupancy trends (including slower declines) in SPA, whereas 21 % showed more negative trends than outside. We conclude that the German SPA network represents target species well approximately two decades after the designation of most SPA, but is currently only effective for a minority of studied target species.Our results contribute to mounting evidence of mixed effectiveness of the Natura 2000 network to maintain populations of target species in Europe. We therefore call for greater conservation efforts, especially for declining species. Our results can help to define priority species and initiate or optimize species-specific management. Thus, semi-structured data have the potential to inform national impact assessments when data from structured monitoring programs are lacking.