Climate warming is expected to induce soil organic carbon losses in mountain soils that result, in turn, in reduced soil fertility, reduced water storage capacity and positive feedback on climate change. Here we combine two independent sets of measurements of soil organic carbon from forest soils in the German Alps—repeated measurements from 1976 to 2010 and from 1987 to 2011—to show that warming has caused a 14% decline in topsoil organic carbon stocks. The decreases in soil carbon occurred over a period of significant increases in six-month summer temperatures, with the most substantial decreases occurring at sites with large changes in mean annual temperature. Organic carbon stock decreases were largest—on average 32%—in forest soils with initial topsoil organic carbon stocks greater than 8 kg C m−2, which can be found predominantly on calcareous bedrock. However, organic carbon stocks of forest soils with lower initial carbon stocks, as well as soils under pasture or at elevations above 1,150 m, have not changed significantly. We conclude that warming is the most likely reason for the observed losses of soil organic carbon, but that site, land use and elevation may ameliorate the effects of climate change. Soil carbon concentrations are sensitive to climate warming. Pairs of measurements of forest soil carbon stocks in the German Alps reveal that topsoil carbon concentrations declined as air temperatures rose between 1976 and 2011.