1. Semi-natural open habitats in northwestern Europe are highly prioritized for conservation and optimization of management planning is essential for continued protection of their diversity. We evaluate whether current management practices, which consist mainly of summer grazing by livestock, are sufficient to maintain plant species composition in a stable state across semi-natural areas in Denmark, or if shifts in functional composition are taking place. Further, we investigate important drivers of any on-going changes through trait differences between winner and loser species. 2. Using a dataset of 6513 annually inventoried (2004–2010) vegetation plots from 202 semi-natural NATURA 2000 protected areas, we assessed changes in cover of all plant species and, using boosted regression trees, whether winners and losers differ in regard to autecological characteristics and traits. 3. There were consistent changes in cover for 123 out of 603 species across the six-year study period, with more species losing than winning (78 versus 45). Winner and loser species were strongly differentiated by competition-related traits, but traits related to soil nutrients and soil moisture also had some importance. Generally, our results indicate a trend towards a species composition consisting of taller and more competitive species. 4. Synthesis and applications. Despite conservation actions in order to maintain so-called favourable conservation status, vegetation in NATURA 2000 protected areas is still undergoing compositional changes. Overall, autecological characteristics and trait differences between winners and losers match expectations given the contemporary anthropogenic pressures, especially with reduced livestock grazing. Atmospheric nitrogen deposition and increased soil moisture due to reduced drainage might also be involved in observed changes. Current management (i.e. summer grazing by livestock) is insufficient to preserve the diversity of less-competitive, low-statured and stress-tolerant herbaceous species, potentially leading to species losses. Such patterns can thus be expected across semi-natural ecosystems in northwestern Europe and other places where traditional land use (i.e. previous widespread extensive livestock grazing) have been replaced with various degrees of conservation management. A greater focus on returning large grazing herbivores to conservation areas is recommended for the protection of plant species diversity and to counteract on-going changes.