Mountain ecosystems are sensitive indicators of climate change. Long-term studies may be extremely useful in assessing the responses of high-elevation ecosystems to climate change and other anthropogenic drivers. Mountain research sites within the LTER (Long-Term Ecosystem Research) network are representative of various types of ecosystems and span a wide bioclimatic and elevational range. Here, we present a synthesis and a review of the main results from long-term ecological studies in mountain ecosystems at 20 LTER sites in Italy, Switzerland and Austria. We analyzed a set of key climate parameters, such as temperature and snow cover duration, in relation to vascular species composition, plant traits, abundance patterns, pedoclimate, nutrient dynamics in soils and water, phenology and composition of freshwater biota. The overall results highlight the rapid response of mountain ecosystems to climate change. As temperatures increased, vegetation cover in alpine and subalpine summits increased as well. Years with limited snow cover duration caused an increase in soil temperature and microbial biomass during the growing season. Effects on freshwater ecosystems were observed, in terms of increases in solutes, decreases in nitrates and changes in plankton phenology and benthos communities. This work highlights the importance of comparing and integrating long-term ecological data collected in different ecosystems, for a more comprehensive overview of the ecological effects of climate change. Nevertheless, there is a need for i) adopting co-located monitoring site networks to improve our ability to obtain sound results from cross-site analysis, ii) carrying out further studies, with fine spatial and temporal resolutions to improve understanding of responses to extreme events, and iii) increasing comparability and standardizing protocols across networks to clarify local from global patterns.