Upward shifts of mountain vegetation lag behind rates of climate warming, partly related to interconnected changes belowground. Here, we unravel above- and belowground linkages by drawing insights from short-term experimental manipulations and elevation gradient studies. Soils will likely gain carbon in early successional ecosystems, while losing carbon as forest expands upward, and the slow, high-elevation soil development will constrain warming-induced vegetation shifts. Current approaches fail to predict the pace of these changes and how much they will be modified by interactions among plants and soil biota. Integrating mountain soils and their biota into monitoring programs, combined with innovative comparative and experimental approaches, will be crucial to overcome the paucity of belowground data and to better understand mountain ecosystem dynamics and their feedbacks to climate.