Biodiversity assessments for conservation planning are often restricted to a limited set of species. This is also the case in the context of Natura 2000, where surveys focus strongly on vegetation and selected vertebrate species. Without cross-taxon congruence, however, this approach does not guarantee that the relevant aspects of biodiversity are appropriately represented. We here assess the diversity of vascular plants, carabid beetles and spiders in mountain grasslands of the European Alps. We address the questions whether there are distinct species assemblages in different habitats and whether these assemblages show sufficient cross-taxon congruence. Furthermore, we test whether habitats that are protected based on vegetation characteristics also inhabit an arthropod fauna with highest conservation value. We found only weak agreement in assemblage composition and no positive correlation in species richness across the three focal taxa. Furthermore, we found a negative correlation between species richness of plants and carabids, indicating opposing taxon-specific responses to habitat differences and land use intensity. Species richness was higher at protected sites for plants, but not for carabids and spiders. This applied also to the subset of species with highest conservation value. Our results show that prioritisation of sites for conservation based solely on vegetational aspects does not necessarily coincide with important sites for arthropods. This calls for a multi-taxon approach in conservation planning to cover more of the endangered and range-restricted species. Species- and surrogate-based conservation efforts, like the Natura 2000 directive, should therefore be extended to embrace the diversity of arthropods.