Many migratory taxa have been declining over recent decades. Although protected areas are considered a cornerstone for conserving migrants, assessing the protection of migratory species is challenging due to their dynamic distributions. Here, we use citizen science (EuroBirdPortal) data on species occurrence and Spatio-Temporal Exploratory Modelling (STEM) to assess how 30 passerine and near passerine species’ weekly distributions overlap with protected areas in Europe and whether this matches stated policy protection targets. Based on the 2020 Convention on Biodiversity (CBD) target, 13 of our 30 species were inadequately covered by protected areas for some, or all, of the European part of their lifecycle; none were adequately covered under the 2030 CBD target. Species with a farmland habitat preference had a lower percentage of their summed occurrence protected than groups with other habitat preferences. The percentage of a species’ summed occurrence in a protected area was positively correlated with long-term population trends, even after accounting for range size, breeding habitat, migration distance and body mass, suggesting a positive influence of protected areas on long-term trends. This emphases the positive contribution that expanding the protected area system for migratory land birds could play for their future conservation.