Biodiversity is currently experiencing an accelerated decline in terms of species and populations, mainly because of habitat loss. The designation of protected areas has therefore become essential for biodiversity conservation. However, compelling evidence for the long-term effectiveness of protected areas in maintaining species diversity is still scarce, especially for plant species, as analyses are often hampered by the limited availability of informative datasets from different time periods. Here we analysed the effectiveness of Swiss protected areas in maintaining vascular plant species typical for two habitat types, namely wetlands and dry grasslands. Furthermore, we tested whether the effect of protected areas on species persistence varies between low (<1000 m a.s.l.) and high elevations (≥1000 m a.s.l.). Data included several thousand historical occurrences, which were re-surveyed after 2002 at the scale of square kilometres. For each re-surveyed species, we identified the square kilometres where it had disappeared and those where it still occurred. We found that the amount of protected area within the square kilometres had a positive effect on the persistence of plant species in the studied habitat types. The effect, however, primarily occurred at low elevations, and even in square kilometres with the largest amount of protected area species declines were still observed. While protected areas at higher elevations are often embedded in a less intensively used matrix, which provides small habitat patches for threatened species, protected areas at lower elevations are often islands within an inhospitable, intensively managed matrix. This explains why protected areas at higher elevations are less important for the persistence of species within square kilometres studied here. Moreover, wetlands and dry grasslands have suffered from changes in land use or heavy exploitation during the past centuries, especially at lower elevations, with ongoing losses of species and populations occurring even within protected areas. Protected areas thus decelerate the landscape-scale loss of species but (apparently) do not fully stop it.