Alpine pastures are agricultural systems with a high provision of ecosystem services, which include carbon (C) stocking. Particularly, the soil organic C (SOC) stocks of Alpine pastures may play a pivotal role in counteracting global climate change. Even if the importance of pasture SOC has been stated by several research studies, especially by comparing different land uses, little is known about the role of plant species composition. We studied a wide sample of 324 pastures in the north-western Italian Alps by performing coupled vegetation and soil surveys. Climatic (i.e., mean annual precipitation), topographic (i.e., elevation, slope, southness), vegetation (i.e., the first three dimensions of a non-metric multid imensional scaling—NMDS), and soil (i.e., pH) parameters were considered as independent variables in a generalised linear model accounting for SOC stocks in the 0–30 cm depth. Pasture SOC was significantly affected by precipitation (positively) and by pH (negatively) but not by topography. However, the higher influence was exerted by vegetation through the first NMDS dimension, which depicted a change in plant species along a thermic-altitudinal gradient. Our research highlighted the remarkable importance of vegetation in regulating SOC stocks in Alpine pastures, confirming the pivotal role of these semi-natural agricultural systems in the global scenario of climate change.